Louis BECQUEY / biorseo

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Louis BECQUEY
9bd1c85e 1 parent 1d43ff8f

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......@@ -7,3 +7,4 @@ ILmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/IL/3.2/li
HLmotifDir="/nhome/siniac/lbecquey/Data/RNA/motifs/BGSU/Matlab_results/HL/3.2/lib"
descfolder="/local/local/labo/03_tests_biominserter/No_Redondance_DESC/"
bypdir="/nhome/siniac/lbecquey/Software/BayesPairing/bayespairing/src"
biorseoDir="/nhome/siniac/lbecquey/Software/biorseo"
\ No newline at end of file
......
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>>__'BRANCHPOINT_HELIX_FROM_YEAST_AND_BINDING_SITE_FOR_PHAGE_GA/MS2_COAT_PROTEINS,_NMR,_12_STRUCTURES_'_(PDB_00002)
GGCGUAAGGAUUACCUAUGCC
(((((.(((....))))))))
>>__'LOOP_D/LOOP_E_ARM_OF_E._COLI_5S_RRNA,_NMR,_9_STRUCTURES_'_(PDB_00004)
GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC
(((((((((((((((((((...)))))))))))))))))))
>>__'NMR_STRUCTURE_OF_A_CLASSICAL_PSEUDOKNOT:_INTERPLAY_OF_SINGLE-AND_DOUBLE-STRANDED_RNA,_24_STRUCTURES_'_(PDB_00005)
GGGAGCUCAACUCUCCCCCCCUUUUCCGAGGGUCAUCGGAACCA
(((((.......)))))[[[...((((((]]]...))))))...
>>__'SOLUTION_STRUCTURE_OF_A_SUBSTRATE_FOR_THE_ARCHAEAL_PRE-TRNA_SPLICING_ENDONUCLEASES:_THE_BULGE-HELIX-BULGE_MOTIF,_NMR,_12_STRUCTURES_'_(PDB_00006)
GGGUGACUCCAGAGGUCGAGAGACCGGAGAUAUCACCC
((((((((((...((((....))))))))...))))))
>>__'UGAA_EUKARYOTIC_RIBOSOMAL_RNA_TETRALOOP,_NMR,_13_STRUCTURES_'_(PDB_00007)
GGUGUGAACACC
((((....))))
>>__'HIV-2_TAR-ARGININAMIDE_COMPLEX,_NMR,_20_STRUCTURES_'_(PDB_00010)
GGCCAGAUUGAGCCUGGGAGCUCUCUGGCC
(((((((..((((......)))))))))))
>>__'CIS-ACTING_RNA_REGULATORY_ELEMENT_(HIV-1_TAR),_NMR,_20_STRUCTURES_'_(PDB_00012)
GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
..(((....((((......)))).)))..
>>__'IRON_RESPONSIVE_ELEMENT_RNA_HAIRPIN,_NMR,_15_STRUCTURES_'_(PDB_00013)
GGAGUGCUUCAACAGUGCUUGGACGCUCC
((((((.((.((......)).))))))))
>>__'THE_STRUCTURE_OF_THE_ISOLATED,_CENTRAL_HAIRPIN_OF_THE_HDV_ANTIGENOMIC_RIBOZYME,_NMR,_10_STRUCTURES_'_(PDB_00014)
GGCACCUCCUCGCGGUGCC
(((((((.....)))))))
>>__'HAIRPIN_WITH_AGAU_TETRALOOP,_NMR,_3_STRUCTURES_'_(PDB_00016)
GCUCCAGAUGGAGCG
(((((....))))).
>>__'NMR_STRUCTURE_OF_THE_DIMER_INITIATION_COMPLEX_OF_HIV-1_GENOMIC_RNA,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00018)
GGCAAUGAAGCGCGCACGUUGCCGGCAAUGAAGCGCGCACGUUGCC
(((((((.[[..[[[[)))))))(((((((.]]]]..]])))))))
>>__'S8_RRNA_BINDING_SITE_FROM_E._COLI,_NMR,_6_STRUCTURES_'_(PDB_00019)
GGGAUACUGCUUCGGUAAGUCCC
((((..((((....)).))))))
>>__'RNA_LOOP-LOOP_COMPLEX:_THE_COLE1_INVERTED_LOOP_SEQUENCE,_NMR,_8_STRUCTURES_'_(PDB_00020)
GGCAACGGAUGGUUCGUUGCCGCACCGAACCAUCCGGUGC
((((((([[[[[[[)))))))((((((]]]]]]]))))))
>>__'SL3_HAIRPIN_FROM_THE_PACKAGING_SIGNAL_OF_HIV-1,_NMR,_11_STRUCTURES_'_(PDB_00021)
GGACUAGCGGAGGCUAGUCC
((((((((....))))))))
>>__'HIV-1_RNA_A-RICH_HAIRPIN_LOOP_'_(PDB_00022)
GGCGACGGUGUAAAAAUCUCGCC
(((((.((((....)))))))))
>>__'STABILIZATION_OF_THE_ANTICODON_STEM-LOOP_OF_TRNALYS,3_BY_AN_A+C_BASE_PAIR_AND_BY_PSEUDOURIDINE,_NMR,_1_STRUCTURE_'_(PDB_00024)
UCAGACUUUUAAUCUGA
((((((.....))))))
>>__'STABILIZATION_OF_THE_ANTICODON_STEM-LOOP_OF_TRNALYS,3_BY_AN_A+C_BASE_PAIR_AND_BY_PSEUDOURIDINE,_NMR,_1_STRUCTURE_'_(PDB_00025)
UCAGACUUUUAAUCUGA
(((((((...)))))))
>>__'STRUCTURE_OF_THE_RIBOZYME_SUBSTRATE_HAIRPIN_OF_NEUROSPORA_VS_RNA._A_CLOSE_LOOK_AT_THE_CLEAVAGE_SITE_'_(PDB_00040)
GUGCGAAGACGAAAGUCCGAGCGC
((((((((((....))))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_PSEUDOKNOT_OF_SRV-1_RNA,_INVOLVED_IN_RIBOSOMAL_FRAMESHIFTING_'_(PDB_00041)
GCGGCCAGCUCCAGGCCGCCAAACAAUAUGGAGCAC
((((((.[[[[[[)))))).........]]]]]]..
>>__'NMR_ANALYSIS_OF_HELIX_I_FROM_THE_5S_RNA_OF_ESCHERICHIA_COLI_'_(PDB_00048)
UUGCCUGGCGGCAACUGCCAGGCAU
..(((((((((...)))))))))..
>>__'NMR_STRUCTURE_OF_STEM_LOOP_SL2_OF_THE_HIV-1_PSI_RNA_PACKAGING_SIGNAL_REVEALS_A_NOVEL_A-U-A_BASE-TRIPLE_PLATFORM_'_(PDB_00051)
GGCGACUGGUGAGUACGCC
(((((((....)).)))))
>>__'CRYSTAL_STRUCTURE_OF_A_BIOTIN-BINDING_RNA_PSEUDOKNOT_'_(PDB_00053)
ACCGUCAGAGGACACGGUUAAAAAGUCCUC
[[[[[..((((((]]]]]......))))))
>>__'SOLUTION_STRUCTURE_OF_THE_KISSING_DIMER_OF_H3_GACG_STEM-_LOOP_IN_THE_5\'-END_DIMERIZATION_SIGNAL_OF_MOLONEY_MURINE_LEUKEMIA_VIRUS_GENOMIC_RNA_'_(PDB_00056)
GGUGGGAGACGUCCCACCGGUGGGAGACGUCCCACC
(((((((..[[)))))))(((((((..]])))))))
>>__'SOLUTION_STRUCTURE_OF_THE_RNASE_P_RNA_(M1_RNA)_P4_STEM_OLIGORIBONUCLEOTIDE_'_(PDB_00057)
GGAAGUCCGGUCUUCGGACCGGCUUCC
(((((.(((((......))))))))))
>>__'SOLUTION_STRUCTURE_OF_RNASE_P_RNA_(M1_RNA)_P4_STEM_OLIGORIBONUCLEOTIDE_COMPLEXED_WITH_COBALT_(III)_HEXAMINE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00059)
GGAAGUCCGGUCUUCGGACCGGCUUCC
(((((.(((((......))))))))))
>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_RNA_DOMAIN_IIID_'_(PDB_00065)
GGCCGAGUAGUGUUGGGUCGCGAAAGGCC
.(((((.(((((......)))))))))).
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_TRNA(LYS3)_WITH_T6A_MODIFICATION_AT_POSITION_37_'_(PDB_00068)
GCAGACUUUUAAUCUGC
((((((.....))))))
>>__'NMR_STRUCTURE_OF_THE_690_LOOP_OF_16_S_RRNA_OF_E._COLI_'_(PDB_00069)
GGCGGUGAAAUGCC
(((((....)))))
>>__'NMR_VALIDATED_MODEL_OF_DOMAIN_IIID_OF_HEPATITIS_C_VIRUS_INTERNAL_RIBOSOME_ENTRY_SITE_'_(PDB_00073)
GCCGAGUAGUGUUGGGUCGCGAAAGGC
(((((.(((((......))))))))))
>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAACU_AS_PART_OF_HAIRPIN_R(GCGUUAACUCGCA)_'_(PDB_00083)
GCGUUAACUCGCA
((((....)))).
>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAAGU_AS_PART_OF_HAIRPIN_R(GCGUUAAGUCGCA)_'_(PDB_00084)
GCGUUAAGUCGCA
((((....)))).
>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAAUU_AS_PART_OF_HAIRPIN_R(GCGUUAAUUCGCA)_'_(PDB_00085)
GCGUUAAUUCGCA
((((....)))).
>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UUAAAU_AS_PART_OF_HAIRPIN_R(GCGUUAAAUCGCA)_'_(PDB_00086)
GCGUUAAAUCGCA
((((....)))).
>>__'SOLUTION_STRUCTURE_OF_RNA_HAIRPIN_LOOP_UCAAUU_AS_PART_OF_HAIRPIN_R(GCGUCAAUUCGCA)_'_(PDB_00087)
GCGUCAAUUCGCA
((((....)))).
>>__'SOLUTION_STRUCTURE_OF_THE_VS_RIBOZYME_SUBSTRATE_STEM-LOOP_'_(PDB_00088)
GGUGCGAAGGGCGUCGUCGCCCCGAGCGCC
((((((((((((......))))))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_A_LOOP_OF_23S_RIBOSOMAL_RNA_'_(PDB_00089)
GGCUGGCUGUUCGCCAGCC
((((((((...))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_A_LOOP_OF_23S_RIBOSOMAL_RNA._'_(PDB_00090)
GGCUGGCUGUUCGCCAGCC
((((((((...))))))))
>>__'THE_SOLUTION_STRUCTURE_OF_THE_MUTANT_STEM_LOOP_C_5\'GUA3\'_TRILOOP_OF_BROME_MOSAIC_VIRUS_(+)_STRAND_RNA_'_(PDB_00091)
GGUGCGUAGCACC
(((((...)))))
>>__'THE_SOLUTION_STRUCTURE_OF_THE_MAJOR_FAMILY_OF_THE_MUTANT_STEM_LOOP_C_5\'UUA3\'_TRILOOP_OF_BROME_MOSAIC_VIRUS_(+)_STRAND_RNA_'_(PDB_00092)
GGUGCUUAGCACC
(((((...)))))
>>__'THE_SOLUTION_STRUCTURE_OF_THE_MINOR_FAMILY_OF_THE_MUTANT_STEM_LOOP_C_5\'UUA3\'_TRILOOP_OF_BROME_MOSAIC_VIRUS_(+)_STRAND_RNA_'_(PDB_00093)
GGUGCUUAGCACC
(((((...)))))
>>__'CRYSTAL_STRUCTURE_ANALYSIS_OF_A_TRNA-NEOMYCIN_COMPLEX_'_(PDB_00095)
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGACUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
(((((((..((((........))))(((((........)))))....(((((.......))))))))))))....
>>__'NMR_STRUCTURE_OF_HCV_IRES_RNA_DOMAIN_IIIC_'_(PDB_00097)
GGGCGUGCCC
(((....)))
>>__'NMR_SOLUTION_STRUCTURE_OF_AN_IN_VITRO_SELECTED_RNA_WHICH_IS_SEQUENCE_SPECIFICALLY_RECOGNIZED_BY_HAMSTER_NUCLEOLIN_RBD12._'_(PDB_00098)
GGCCGAAAUCCCGAAGUAGGCC
((((((..........))))))
>>__'SOLUTION_STRUCTURE_OF_AN_IN_VITRO_SELECTED_RNA_WHICH_IS_SEQUENCE_SPECIFICALLY_RECOGNIZED_BY_RBD12_OF_HAMSTER_NUCLEOLIN.SNRE_(ANTI)_'_(PDB_00099)
GGCCGAAAUCCCGAAGUAGGCC
((((((..........))))))
>>__'SOLUTION_STRUCTURE_OF_AN_RNA_HAIRPIN_FROM_HRV-14_'_(PDB_00100)
GGUACUAUGUACCA
(((((...))))).
>>__'SOLUTION_STRUCTURE_OF_THE_UNMODIFIED_ANTICODON_STEM-LOOP_FROM_E._COLI_TRNA(PHE)_'_(PDB_00103)
GGGGAUUGAAAAUCCCC
(((((((...)))))))
>>__'NMR_STRUCTURE_OF_THE_LP5.1_HAIRPIN_FROM_BACILLUS_RNASE_P_RNA_REFINED_WITH_RESIDUAL_DIPOLAR_COUPLINGS_'_(PDB_00108)
GGCGGUGCUGAGAUGCCCGUC
(((((.((......)))))))
>>__'NMR_STRUCTURE_OF_THE_LP5.1_HAIRPIN_FROM_BACILLUS_RNASE_P_RNA_REFINED_WITHOUT_RESIDUAL_DIPOLAR_COUPLINGS_'_(PDB_00109)
GGCGGUGCUGAGAUGCCCGUC
(((((.((......)))))))
>>__'SOLUTION_STRUCTURE_OF_HIV-1LAI_MUTATED_SL1_HAIRPIN_'_(PDB_00110)
CUUGCUGAAGCACGCACGGCAAG
(((((((.........)))))))
>>__'THE_SOLUTION_STRUCTURE_OF_THE_MUTANT_5\'AUG3\'_TRILOOP_IN_THE_RNA_PROMOTER_REGION_OF_THE_BROME_MOSAIC_VIRUS_GENOMIC_(+)-_RNA_'_(PDB_00114)
GGUGCAUGGCACC
((((.....))))
>>__'STRUCTURE_OF_AGUU_RNA_TETRALOOP,_NMR,_20_STRUCTURES_'_(PDB_00118)
GGUUCAGUUGAACC
(((((....)))))
>>__'NMR_STRUCTURE_OF_A_RIBOSOMAL_RNA_HAIRPIN_CONTAINING_A_CONSERVED_CUCAA_PENTALOOP_'_(PDB_00119)
GGACCCGGGCUCAACCUGGGUCC
((((((((((...))))))))))
>>__'HIV-1(MAL)_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00123)
UUUGCUGAGGUGCACACAGCAAUUUUGCUGAGGUGCACACAGCAAUUUUGCUGAGGUGCACACAGCAAUUUUGCUGAGGUGCACACAGCAAU
..(((((..[[[[[[.)))))..(((((((..]]]]]].)))))))..(((((..[[[[[[.)))))..(((((((..]]]]]].)))))))
>>__'CONFORMATION_OF_AN_RNA_PSEUDOKNOT_FROM_MOUSE_MAMMARY_TUMOR_VIRUS,_NMR,_1_STRUCTURE_'_(PDB_00124)
GGCGCAGUGGGCUAGCGCCACUCAAAAGCCCG
((((((..[[[[.))))))........]]]].
>>__'TAR-TAR_"KISSING"_HAIRPIN_COMPLEX_DERIVED_FROM_THE_HIV_GENOME,_NMR,_1_STRUCTURE_'_(PDB_00128)
GAGCCCUGGGAGGCUCGCUGUUCCCAGACAGC
((((([[[[..)))))(((((.]].]])))))
>>__'SOLUTION_STRUCTURE_OF_THE_UNMODIFIED_ANTICODON_STEM-LOOP_FROM_E._COLI_TRNA(PHE)_'_(PDB_00129)
GGGGAUUGAAAAUCCCC
(((((((...)))))))
>>__'STRUCTURE_OF_THE_HISTONE_MRNA_HAIRPIN_REQUIRED_FOR_CELL_CYCLE_REGULATION_OF_HISTONE_GENE_EXPRESSION_'_(PDB_00130)
GGAAGGCCCUUUUCAGGGCCACCC
....((((((....))))))....
>>__'SOLUTION_NMR_STRUCTURE_OF_AN_ANALOG_OF_THE_YEAST_TRNA_PHE_T_STEM_LOOP_CONTAINING_RIBOTHYMIDINE_AT_ITS_NATURALLY_OCCURRING_POSITION_'_(PDB_00131)
CUGUGUUCGAUCCACAG
(((((.......)))))
>>__'A_MUTANT_RNA_PSEUDOKNOT_THAT_PROMOTES_RIBOSOMAL_FRAMESHIFTING_IN_MOUSE_MAMMARY_TUMOR_VIRUS,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00133)
GGCGCAGUGGGCUAGCGCCACUCAAAGGCCCG
(((((...[[[[[.))))).......]]]]].
>>__'PEMV-1_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_15_LOWEST_ENERGY_STRUCTURES_'_(PDB_00134)
UCCGGUCGACUCCGGAGAAACAAAGUCA
(((((..[[[.)))))........]]].
>>__'PEMV-1_P1-P2_FRAMESHIFTING_PSEUDOKNOT_REGULARIZED_AVERAGE_STRUCTURE_'_(PDB_00135)
UCCGGUCGACUCCGGAGAAACAAAGUCA
(((((..[[..))))).........]].
>>__'ATOMIC_RESOLUTION_CRYSTAL_STRUCTURE_OF_A_VIRAL_RNA_PSEUDOKNOT_'_(PDB_00138)
GGCGCGGCACCGUCCGCGGAACAAACGG
..(((((..[[[.))))).......]]]
>>__'LOW_RESOLUTION_CRYSTAL_STRUCTURE_OF_A_VIRAL_RNA_PSEUDOKNOT_'_(PDB_00139)
GGCGCGGCACCGUCCGCGGAACAAACGG
..(((((..[[[.))))).......]]]
>>__'SOLUTION_STRUCTURE_OF_THE_U6_INTRAMOLECULAR_STEM-LOOP_RNA_'_(PDB_00141)
GGUUCCCCUGCAUAAGGAUGAACC
((((((((((...))))).)))))
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_YEAST_TRNA-PHE_WITH_4_MODIFICATIONS_(OMC32_OMG34_1MG37_5MC40)_'_(PDB_00147)
CCAGACUGAAGAUCUGG
((((((.....))))))
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_YEAST_TRNA-PHE_WITH_3_MODIFICATIONS_(OMC32_OMG34_M5C40)_'_(PDB_00148)
CCAGACUGAAGAUCUGG
((((((.....))))))
>>__'CRYSTAL_STRUCTURE_ANALYSIS_OF_A_26MER_RNA_MOLECULE,_REPRESENTING_A_NEW_RNA_MOTIF,_THE_HOOK-TURN_'_(PDB_00155)
CCAUGCGAACCGCGAUCCUAGUGUGG
((((((((..........))))))))
>>__'STRUCTURE_OF_23S_RIBOSOMAL_RNA_HAIRPIN_35_'_(PDB_00160)
GGCGUAACGUUGAAAAGUUACGCC
(((((((((......)))))))))
>>__'SOLUTION_STRUCTURE_OF_B._SUBTILIS_T_BOX_ANTITERMINATOR_RNA_'_(PDB_00168)
GAGGGUGGAACCGCGCGCGUCCCUC
((((........((....)).))))
>>__'SOLUTION_STRUCTURE_OF_THE_P2B_HAIRPIN_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00171)
GGGCUGUUUUUCUCGCUGACUUUCAGCCCC
((((((((((((.....)))))))))))).
>>__'IRON_RESPONSIVE_ELEMENT_RNA_HAIRPIN,_NMR,_15_STRUCTURES_'_(PDB_00172)
GGAGUGCUUCAACAGUGCUUGGACGCUCC
((((((.(((((......)))))))))))
>>__'U80G_U6_INTRAMOLECULAR_STEM-LOOP_RNA_FROM_SACCHAROMYCES_CEREVISIAE_'_(PDB_00173)
GGUUCCCCUGCAUAAGGAGGAACC
((((((((((...)))).))))))
>>__'SOLUTION_STRUCTURE_OF_THE_S._CEREVISIAE_U6_INTRAMOLECULAR_STEM-LOOP_CONTAINING_AN_SP_PHOSPHOROTHIOATE_AT_NUCLEOTIDE_U80_'_(PDB_00177)
GGUUCCCCUGCAUAAGGAUGAACC
((((((((((...))))).)))))
>>__'P6.1_STEM_LOOP_FROM_THE_ACTIVATION_DOMAIN_OF_HTR_'_(PDB_00180)
GAGAGUUGGGCUCUC
((((((...))))))
>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_DOMAIN_IIB_'_(PDB_00184)
GGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGCC
(((((((((((((.......))))))).))))))
>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_DOMAIN_II_'_(PDB_00185)
GGCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGCC
(((((.((((.....((((((.((((((((..(((((.......)))))...)))))))).)).)))))))))))))
>>__'SOLUTION_STRUCTURE_OF_HCV_IRES_DOMAIN_II_(MINIMIZED_AVERAGE_STRUCTURE)_'_(PDB_00186)
GGCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGCC
(((((.((((.....((((((((((((((((((((((.......))))))).))))))))))).)))))))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_DYSKERATOSIS_CONGENITA_MUTANT_P2B_HAIRPIN_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00191)
GGCUCUCAGUGAGCC
(((((.....)))))
>>__'NMR_STRUCTURE_OF_TAU_EXON_10_SPLICING_REGULATORY_ELEMENT_RNA_'_(PDB_00197)
GGCAGUGUGAGUACCUUCACACGUC
....(((((((....)))))))...
>>__'NMR_STRUCUTRE_OF_5\'-R(GGACACGAAAUCCCGAAGUAGUGUCC)-3\'_:_AN_RNA_HAIRPIN_CONTAINING_THE_IN_VITRO_SELECTED_CONSENSUS_SEQUENCE_FOR_NUCLEOLIN_RBD12_'_(PDB_00201)
GGACACGAAAUCCCGAAGUAGUGUCC
((((((((((.....)).))))))))
>>__'24-MER_RNA_HAIRPIN_COAT_PROTEIN_BINDING_SITE_FOR_BACTERIOPHAGE_R17_(NMR,_MINIMIZED_AVERAGE_STRUCTURE)_'_(PDB_00206)
GGGACUGACGAUCACGCAGUCUAU
.((((((.((....))))))))..
>>__'THE_STRUCTURE_OF_AN_RNA_PSEUDOKNOT_THAT_CAUSES_EFFICIENT_FRAMESHIFTING_IN_MOUSE_MAMMARY_TUMOR_VIRUS_'_(PDB_00209)
GGCGCAGUGGGCUAGCGCCACUCAAAAGGCCCAU
[[[[[..((((((.]]]]]........)))))).
>>__'FIRST_STEM_LOOP_OF_THE_SL1_RNA_FROM_CAENORHABDITIS_ELEGANS,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00216)
UUACCCAAGUUUGAGGUAA
(((((((....)).)))))
>>__'FIRST_STEM_LOOP_OF_THE_SL1_RNA_FROM_CAENORHABDITIS_ELEGANS,_NMR,_16_STRUCTURES_'_(PDB_00217)
UUACCCAAGUUUGAGGUAA
(((((((....)).)))))
>>__'REFINED_SOLUTION_STRUCTURE_OF_THE_S._CEREVISIAE_U6_INTRAMOLECULAR_STEM_LOOP_(ISL)_RNA_USING_RESIDUAL_DIPOLAR_COUPLINGS_(RDCS)_'_(PDB_00218)
GGUUCCCCUGCAUAAGGAUGAACC
((((((((((...))))).)))))
>>__'SOLUTION_STRUCTURE_OF_ITALY1_("INITIATOR_TRNA_ANTICODON_LOOP_FROM_YEAST"),_AN_UNMODIFIED_21-NT_RNA_WITH_THE_SEQUENCE_OF_THE_ANTICODON_STEM-LOOP_OF_YEAST_INITIATOR_TRNA_'_(PDB_00219)
GGCAGGGCUCAUAACCCUGCC
(((((((.......)))))))
>>__'STEM_LOOP_IIA_FROM_U2SNRNA_OF_SACCHAROMYCES_CEREVISIAE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00224)
GGUCAGUGUAACAACUGACC
((((((((....))))))))
>>__'STRUCTURE_OF_AN_RNA_HAIRPIN_LOOP_WITH_A_5\'-CGUUUCG-3\'_LOOP_MOTIF_BY_HETERONUCLEAR_NMR_SPECTROSCOPY_AND_DISTANCE_GEOMETRY,_15_STRUCTURES_'_(PDB_00225)
GGCGUACGUUUCGUACGCC
(((((((.....)))))))
>>__'CONSERVED_RNA_COMPONENT_OF_THE_PEPTIDYL_TRANSFERASE_CENTER,_NMR,_33_STRUCTURES_'_(PDB_00226)
GACUGGGGCGGUC
(((((...)))))
>>__'YEAST_INITIATOR_TRNA_'_(PDB_00229)
AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAACCGAGCGGCGCUACCA
(((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))))....
>>__'GAAA_RNA_TETRALOOP,_NMR,_10_STRUCTURES_'_(PDB_00231)
GGGCGAAAGCCU
(((......)))
>>__'SOLUTION_NMR_STRUCTURE_OF_A_SUBSTRATE_FOR_THE_ARCHAEAL_PRE-_TRNA_SPLICING_ENDONUCLEASES:_THE_BULGE-HELIX-BULGE_MOTIF,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00240)
GGGUGACUCCAGAGGUCGAGAGACCGGAGAUAUCACCC
((((((((((...((((....))))))))...))))))
>>__'RNA_LOOP-LOOP_COMPLEX:_THE_COLE1_INVERTED_LOOP_SEQUENCE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00241)
GGCAACGGAUGGUUCGUUGCCGCACCGAACCAUCCGGUGC
((((((([[[[[[[)))))))((((((]]]]]]]))))))
>>__'AN_INVESTIGATION_OF_THE_STRUCTURE_OF_THE_PSEUDOKNOT_WITHIN_THE_GENE_32_MESSENGER_RNA_OF_BACTERIOPHAGE_T2_USING_HETERONUCLEAR_NMR_METHODS_'_(PDB_00243)
GCUGACCAGCUAUGAGGUCAUACAUCGUCAUAGCAC
..[[[[[.(((((((]]]]].......)))))))..
>>__'STEM_LOOP_IIA_FROM_U2_SNRNA_OF_SACCHAROMYCES_CEREVISIAE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00245)
GGUCAGUGUAACAACUGACC
((((((((....))))))))
>>__'RNA_PSEUDOKNOT_WITH_3D_DOMAIN_SWAPPING_'_(PDB_00256)
UCCGAAGUGCAACGGGAAAAUGCACU
.((((......))))...........
>>__'STRUCTURE_OF_THE_3\'_HAIRPIN_OF_THE_TYMV_PSEUDOKNOT:_PREFORMATION_IN_RNA_FOLDING_'_(PDB_00258)
GGUUCCGAGGGUCAUCGGAACCA
((((((((......)))))))).
>>__'CRYSTAL_STRUCTURE_OF_AN_RNA_PSEUDOKNOT_FROM_BEET_WESTERN_YELLOW_VIRUS_INVOLVED_IN_RIBOSOMAL_FRAMESHIFTING_'_(PDB_00269)
GGCGCGGCACCGUCCGCGGAACAAACGG
..(((((..[[[.))))).......]]]
>>__'STRUCTURE_OF_THE_HIV-1_NUCLEOCAPSID_PROTEIN_BOUND_TO_THE_SL3_PSI-RNA_RECOGNITION_ELEMENT,_NMR,_25_STRUCTURES_'_(PDB_00285)
GGACUAGCGGAGGCUAGUCC
((((((((....))))))))
>>__'SATELLITE_TOBACCO_MOSAIC_VIRUS/RNA_COMPLEX_'_(PDB_00286)
AAAAAAAAAAUUUUUUUUUU
..((((((...))))))...
>>__'LOOP_D/LOOP_E_ARM_OF_ESCHERICHIA_COLI_5S_RRNA,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00288)
GGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGCC
(((((((((((((((((((...)))))))))))))))))))
>>__'SOLUTION_STRUCTURE_OF_PHAGE_P22_N_PEPTIDE-BOX_B_RNA_COMPLEX,_NMR,_20_STRUCTURES_'_(PDB_00289)
GCGCUGACAAAGCGC
((((((...))))))
>>__'CRYSTAL_STRUCTURE_OF_THE_SPLICEOSOMAL_U2B\'\'-U2A\'_PROTEIN_COMPLEX_BOUND_TO_A_FRAGMENT_OF_U2_SMALL_NUCLEAR_RNA_'_(PDB_00293)
CCUGGUAUUGCAGUACCUCCAGGUCCUGGUAUUGCAGUACCUCCAGGU
((((((...........)))))).((((((...........)))))).
>>__'HIV-2_TRANS_ACTIVATING_REGION_RNA_COMPLEX_WITH_ARGININAMIDE,_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00299)
GGCCAGAUUGAGCCUGGGAGCUCUCUGGCC
(((((((..((((......)))))))))))
>>__'BACTERIOPHAGE_MS2_CAPSID_PROTEIN/RNA_COMPLEX_'_(PDB_00303)
AUGAGGAUUACCCAUGUGAGGAUUACCC
(((.((....)))))....((....)).
>>__'STRUCTURE_OF_A_MS2_COAT_PROTEIN_MUTANT_IN_COMPLEX_WITH_AN_RNA_OPERATOR_'_(PDB_00304)
AUGAGGAUUACCCAUGAUGAGGAUUACCCA
(((.((....)))))..((.((....))))
>>__'ARG-BOUND_TAR_RNA,_NMR_'_(PDB_00306)
GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
..((((...((((......))))))))..
>>__'U1A-UTRRNA,_NMR,_31_STRUCTURES_'_(PDB_00312)
GGCAGAGUCCUUCGGGACAUUGCACCUGCC
(((((.((((....)))).......)))))
>>__'BOVINE_IMMUNODEFICIENCY_VIRUS_TAT-TAR_COMPLEX,_NMR,_5_STRUCTURES_'_(PDB_00317)
GGCUCGUGUAGCUCAUUAGCUCCGAGCC
((((((...((((....)))).))))))
>>__'HEPATITIS_DELTA_VIRUS_RIBOZYME_'_(PDB_00335)
GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGCGAAUGGGAC
(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_5S_RRNA_E-LOOP/L25_COMPLEX_'_(PDB_00339)
GGACCGAUGGUAGUGUCUUCGGAUGCGAGAGUAGGUC
.((((((((((((((((....))))))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_E.COLI_RIBOSOMAL_PROTEIN_L25_COMPLEXED_WITH_A_5S_RRNA_FRAGMENT_AT_1.8_A_RESOLUTION_'_(PDB_00341)
CCCAUGCGAGAGUAGGGACUGCCGAUGGUAGUGUGGGG
((((((((((((((((.....)))))))))))))))).
>>__'U1A_SPLICEOSOMAL_PROTEIN/HEPATITIS_DELTA_VIRUS_GENOMIC_RIBOZYME_COMPLEX_'_(PDB_00346)
GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGCGAAUGGGAC
(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CORE_OF_THE_ALU_DOMAIN_OF_THE_MAMMALIAN_SRP_'_(PDB_00352)
GGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC
(((((((((((((..[[))))))))....((((.]].....)))))))))
>>__'CRYSTAL_STRUCTURE_OF_NOVA-2_KH3_K-HOMOLOGY_RNA-BINDING_DOMAIN_BOUND_TO_20-MER_RNA_HAIRPIN_'_(PDB_00357)
GAGGACCUAGAUCACCCCUCGAGGACCUAGAUCACCCCUC
(((((..........)))))(((((..........)))))
>>__'STRUCTURAL_BASIS_FOR_RECOGNITION_OF_THE_RNA_MAJOR_GROOVE_IN_THE_TAU_EXON_10_SPLICING_REGULATORY_ELEMENT_BY_AMINOGLYCOSIDE_ANTIBIOTICS_'_(PDB_00361)
GGCAGUGUGAGUACCUUCACACGUC
....((((((......))))))...
>>__'THE_CRYSTAL_STRUCTURE_OF_PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_COGNATE_TRNAPHE_'_(PDB_00362)
GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
>>__'CRYSTAL_STRUCTURE_OF_GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA-GLN_MUTANT_AND_AN_ACTIVE-SITE_INHIBITOR_'_(PDB_00373)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))..(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA_MUTANT_AND_AN_ACTIVE_SITE_INHIBITOR_'_(PDB_00374)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAAGCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))...(((((.......))))))))))).....
>>__'CRYSTAL_STRUCTURE_OF_A_TIGHT-BINDING_GLUTAMINE_TRNA_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00376)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((((...))))))))...(((((.......))))))))))).....
>>__'SOLUTION_STRUCTURE_OF_HTLV-1_PEPTIDE_BOUND_TO_ITS_RNA_APTAMER_TARGET_'_(PDB_00377)
GGGCGCCGGUACGCAAGUACGACGGUACGCUCC
((((((((((((....))))..)))..))))).
>>__'NMR_STRUCTURE_OF_THE_HIV-1_NUCLEOCAPSID_PROTEIN_BOUND_TO_STEM-LOOP_SL2_OF_THE_PSI-RNA_PACKAGING_SIGNAL._IMPLICATIONS_FOR_GENOME_RECOGNITION_'_(PDB_00383)
GGCGACUGGUGAGUACGCC
(((((((....)).)))))
>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00402)
GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
>>__'SOLUTION_STRUCTURE_OF_NUCLEOLIN_RBD12_IN_COMPLEX_WITH_SNRE_RNA_'_(PDB_00407)
GGCCGAAAUCCCGAAGUAGGCC
((((((..........))))))
>>__'COMPLEX_OF_HIV-1_RRE-IIB_RNA_WITH_RSG-1.2_PEPTIDE_'_(PDB_00420)
GGUCUGGGCGCACUUCGGUGACGGUACAGGCC
...((((((((((....))).))).))))...
>>__'STRUCTURAL_BASIS_OF_ANTICODON_LOOP_RECOGNITION_BY_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00425)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
>>__'STRUCTURAL_BASIS_FOR_TRANSFER_RNA_AMINOACEYLATION_BY_ESCHERICHIA_COLI_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00426)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........))).(((((((...))))))).....(((((.......))))))))))).....
>>__'BACTERIOPHAGE_HK022_NUN-PROTEIN-NUTBOXB-RNA_COMPLEX_'_(PDB_00434)
GCCCUGAAAAAGGGC
((((((...))))))
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEAL_TYROSYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA(TYR)_AND_L-TYROSINE_'_(PDB_00474)
CCGGCGGUAGUUCAGCCUGGUAGAACGGCGGACUGUAGAUCCGCAUGUCGCUGGUUCAAAUCCGGCCCGCCGGA
(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))).
>>__'CRYSTAL_STRUCTURE_OF_THE_RIBOTOXIN_RESTRICTOCIN_AND_A_31-_MER_SRD_RNA_INHIBITOR_'_(PDB_00481)
GCGCUCCUCAGUACGAGAGGAACCGGAGCGCGCGCUCCUCAGUACGAGAGGAACCGGAGCGC
((((((((((.(((....)))))))))))))((((((((((.(((....)))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_RIBOTOXIN_RESTRICTOCIN_AND_A_29-MER_SRD_RNA_ANALOG_'_(PDB_00482)
CGCUCCUCAGUACGAUAGGAACCGGAGCGCGCUCCUCAGUACGAUAGGAACCGGAGCG
(((((((((.(((....))))))))))))(((((((((.(((....))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_RIBOTOXIN_RESTRICTOCIN_COMPLEXED_WITH_A_29-MER_SARCIN/RICIN_DOMAIN_RNA_ANALOG_'_(PDB_00483)
CGCUCCUCAGUACGAGAGGAACCGGAGCGCGCUCCUCAGUACGAGAGGAACCGGAGCG
(((((((((.(((....))))))))))))(((((((((.(((....))))))))))))
>>__'HUMAN_SRP19_IN_COMPLEX_WITH_HELIX_6_OF_HUMAN_SRP_RNA_'_(PDB_00487)
GGUGACCUCCCGGGAGCGGGGGACCACUA
((((((((((((....)))))))))))).
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_RNA_HAIRPIN_BINDING_SITE_FOR_THE_HISTONE_STEM-LOOP_BINDING_PROTEIN_'_(PDB_00495)
GGCCCUUUUCAGGGCC
((((((....))))))
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_RNA_HAIRPIN_BINDING_SITE_FOR_THE_HISTONE_STEM-LOOP_BINDING_PROTEIN_'_(PDB_00497)
GGCCCUUUUCAGGGCC
....((....))....
>>__'CRYSTAL_STRUCTURE_OF_THE_E._COLI_PSEUDOURIDINE_SYNTHASE_TRUB_BOUND_TO_A_T_STEM-LOOP_RNA_'_(PDB_00513)
GGCAACGGUUCGAUCCCGUUGC
.(((((((.......)))))))
>>__'RNA_APTAMER_COMPLEXED_WITH_ARGININE,_NMR_'_(PDB_00526)
AGAAGGAGCGUACAGGUAGGUCGCU
.....(((...........)))...
>>__'CRYSTAL_STRUCTURE_OF_T3C_MUTANT_S15_RIBOSOMAL_PROTEIN_IN_COMPLEX_WITH_16S_RRNA_'_(PDB_00535)
GGGCGGCCUUCGGGCUAGACGGUGGGAGAGGCUUCGGCUGGUCCACCCGUGACGCUC
((((.(((....)))...((((((((((.(((....)))))))))).)))...))))
>>__'CRYSTAL_STRUCTURE_OF_THE_SRP19-7S.S_SRP_RNA_COMPLEX_OF_M._JANNASCHII_'_(PDB_00547)
UCGGCGGUGGGGGAGCAUCUCCUGUAGGGGAGAUGUAACCCCCUUUACCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUC
..((((..(((((.(((((((((....)))))))))..)))))....((((((((....((((.(((((....))))).)))).)))))))).))))
>>__'STRUCTURE_OF_TAR_RNA_COMPLEXED_WITH_A_TAT-TAR_INTERACTION_NANOMOLAR_INHIBITOR_THAT_WAS_IDENTIFIED_BY_COMPUTATIONAL_SCREENING_'_(PDB_00553)
GGCCAGAUCUGAGCCUGGGAGCUCUCUGGCC
(((((((...((((......)))))))))))
>>__'DETAILED_ANALYSIS_OF_RNA-PROTEIN_INTERACTIONS_WITHIN_THE_BACTERIAL_RIBOSOMAL_PROTEIN_L5/5S_RRNA_COMPLEX_'_(PDB_00570)
GGCACCUGACCCCAUGCCGAACUCAGAAGUGCCCGGCACCUGACCCCAUGCCGAACUCAGAAGUGCCC
(((((((((....((....)).))))..))))).(((((((((....((....)).))))..))))).
>>__'BIV_TAT_PEPTIDE_(RESIDUES_68-81),_NMR,_MINIMIZED_AVERAGE_STRUCTURE_'_(PDB_00574)
GGCUCGUGUAGCUCAUUAGCUCCGAGCC
((((((...((((....)))).))))))
>>__'LAMBDA3_ELONGATION_COMPLEX_WITH_FOUR_PHOSPHODIESTER_BOND_FORMED_'_(PDB_00588)
GGGGGUAGCCCCCCCC
.((.......))....
>>__'REOVIRUS_POLYMERASE_LAMBDA3_ELONGATION_COMPLEX_WITH_ONE_PHOSPHODIESTER_BOND_FORMED_'_(PDB_00590)
GCUUAGCUCC
((...))...
>>__'SACCHARIDE-RNA_RECOGNITION_IN_THE_NEOMYCIN_B_/_RNA_APTAMER_COMPLEX_'_(PDB_00603)
GGACUGGGCGAGAAGUUUAGUCC
((((((((((...))))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_BACTERIOPHAGE_PHI21_N_PEPTIDE-_BOXB_RNA_COMPLEX_'_(PDB_00617)
GGUUCACCUCUAACCGGGUGAGCC
((((((((((....))))))))))
>>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMINE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00620)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))(((((((.....)))))))....(((((.......))))))))))).....
>>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMATE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00621)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
>>__'MODEL_FOR_THIOSTREPTON_ANTIBIOTIC_BINDING_TO_L11_SUBSTRATE_FROM_50S_RIBOSOMAL_RNA_'_(PDB_00627)
GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC
(((((((((..((((.......))))..)))........((((....)))).))))))
>>__'CRYSTAL_STRUCTURE_OF_THE_TRNA_DOMAIN_OF_TRANSFER-MESSENGER_RNA_IN_COMPLEX_WITH_SMPB_'_(PDB_00637)
GAUUCGACGGGGACUUCGGUCCUCGGACGCGGGUUCGAUUCCCGCUCGACGGGGACUUCGGUCCUCGGA
......((((((((....))))))))..(((((.......)))))...((((((((....)))))))).
>>__'CHEMICAL_TRAPPING_AND_CRYSTAL_STRUCTURE_OF_A_CATALYTIC_TRNA_GUANINE_TRANSGLYCOSYLASE_COVALENT_INTERMEDIATE_'_(PDB_00648)
AGCACGGCUUAAACCGUGCAGCACGGCUUAAACCGUGCUUUU
(((((((......)))))))((((((......))))))....
>>__'CHEMICAL_TRAPPING_AND_CRYSTAL_STRUCTURE_OF_A_CATALYTIC_TRNA_GUANINE_TRANSGLYCOSYLASE_COVALENT_INTERMEDIATE_'_(PDB_00649)
AGCACGGCUGUAAACCGUGCAGCACGGCUUAAACCGUGC
(((((((.......)))))))((((((......))))))
>>__'HIV-1_TAR_RNA/NEOMYCIN_B_COMPLEX_'_(PDB_00664)
GCCAGAUUUGAGCCUGGGAGCUCUCUGGC
((((((...((((......))))))))))
>>__'BACTERIOPHAGE_LAMBDA_N-PROTEIN-NUTBOXB-RNA_COMPLEX_'_(PDB_00668)
GCCCUGAAAAAGGGC
((((((...))))))
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235N_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00669)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((((...))))))))....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235G_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00670)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))(((((((.....)))))))....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_I129T_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00671)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..(((.........)))((((((.......))))))....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA_AND_AN_AMINO_ACID_ANALOG_'_(PDB_00672)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....
>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00673)
GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
>>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00674)
GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC
(((((((..((((.........))))(((((((.....)))))))....(((((.......))))))))))))..
>>__'SOLUTION_STRUCTURE_OF_THE_COMPLEX_FORMED_BY_THE_TWO_N-_TERMINAL_RNA-BINDING_DOMAINS_OF_NUCLEOLIN_AND_A_PRE-RRNA_TARGET_'_(PDB_00691)
GGAUGCCUCCCGAGUGCAUCC
((((((.........))))))
>>__'THE_STRUCTURE_OF_A_RIBOSOMAL_PROTEIN_S8/SPC_OPERON_MRNA_COMPLEX_'_(PDB_00702)
GGACGAUGGCGAAACUGCAUGAGGCAAUUCAUGCAAGUCCCUCGUCCGGACGAUGGCGAAACUGCAUGAGGCAAUUCAUGCAAGUCCCUCGUCC
((((((.((.((..((((((((......)))))).))))))))))))((((((.((.((..((((((((......)))))).))))))))))))
>>__'AVERAGE_SOLUTION_STRUCTURE_OF_A_PSEUDO-5\'-SPLICE_SITE_FROM_THE_NEGATIVE_REGULATOR_OF_SPLICING_OF_ROUS_SARCOMA_VIRUS_'_(PDB_00705)
GGGGAGUGGUUUGUAUCCUUCCC
((((((.((......))))))))
>>__'SOLUTION_STRUCTURE_OF_RESIDUES_907-929_FROM_ROUS_SARCOMA_VIRUS_'_(PDB_00706)
GGGGAGUGGUUUGUAUCCUUCCC
((((((.(((....)))))))))
>>__'HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_MG2+_BOUND_'_(PDB_00714)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_A_C75U_MUTANT_HEPATITIS_DELTA_VIRUS_RIBOZYME_PRECURSOR,_IN_CU2+_SOLUTION_'_(PDB_00715)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_COBALT_HEXAMMINE_SOLUTION_'_(PDB_00716)
AUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
..(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'SOLUTION_STRUCTURE_OF_THE_S._CEREVISIAE_U6_INTRAMOLECULAR_STEM_LOOP_(ISL)_RNA_AT_PH_5.7_'_(PDB_00721)
GGUUCCCCUGCAUAAGGAUGAACC
((((((((((...))))).)))))
>>__'HIGH_RESOLUTION_STRUCTURE_OF_A_PICORNAVIRAL_INTERNAL_CIS-_ACTING_REPLICATION_ELEMENT_'_(PDB_00727)
GGUCAUCGUUGAGAAAACGAAACAGACGGUGGCC
((..(((((................)))))..))
>>__'NMR_STRUCTURE_OF_THE_VS_RIBOZYME_STEM-LOOP_V_RNA_IN_THE_ABSENCE_OF_MULTIVALENT_IONS._'_(PDB_00730)
GCGAGUUGACUACUCGC
((((((.....))))))
>>__'SACCHARIDE-RNA_RECOGNITION_IN_AN_AMINOGLYCOSIDE_ANTIBIOTIC-_RNA_APTAMER_COMPLEX,_NMR,_7_STRUCTURES_'_(PDB_00737)
GGCACGAGGUUUAGCUACACUCGUGCC
(((((((((((....))).))))))))
>>__'CRYSTAL_STRUCTURE_OF_CYSTEINYL-TRNA_SYNTHETASE_BINARY_COMPLEX_WITH_TRNACYS_'_(PDB_00742)
GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA
(((((((..(((.........))).((((((.....))))))....(((((.......))))))))))))....
>>__'CRYSTAL_STRUCTURE_OF_A_COMPLEX_BETWEEN_WT_BACTERIOPHAGE_MS2_COAT_PROTEIN_AND_AN_F5_APTAMER_RNA_STEMLOOP_WITH_2AMINOPURINE_SUBSTITUTED_AT_THE-10_POSITION_'_(PDB_00743)
CCGGGGGAUCACCACGGCGGGGGAUCACCACGG
((((.((....))))))(((.((....))))).
>>__'THE_STRUCTURE_OF_A_RIBOSOMAL_PROTEIN_L1-MRNA_COMPLEX_'_(PDB_00746)
GGGAGUGAAGGAGGCUCGCGAACUCGCGAAGCCGAGAAACUUCACUCCCGGGAGUGAAGGAGGCUCGCGAACUCGCGAAGCCGAGAAACUUCACUCCC
.(((((((((((((((((((....)))).)))))....))))))))))..(((((((((((((((((((....)))).)))))....)))))))))).
>>__'GUANINE_RIBOSWITCH_BOUND_TO_HYPOXANTHINE_'_(PDB_00749)
GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGUCC
(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..)))))))
>>__'REOVIRUS_POLYMERASE_LAMBDA-3_LOCALIZED_BY_ELECTRON_CRYOMICROSCOPY_OF_VIRIONS_AT_7.6-A_RESOLUTION_'_(PDB_00753)
GGGGGUAGCCCCCCCC
.((.......))....
>>__'U1A_MUTANT/RNA_COMPLEX_+_GLYCEROL_'_(PDB_00754)
AAUCCAUUGCACGGAUUAAUCCAUUGCACUCCGGAUUUAAUCCAUUGCACGGAUU
.((((.......)))).(((((..........)))))...(((.......)))..
>>__'DESIGNED_HIV-1_TAR_BINDING_LIGAND_'_(PDB_00755)
GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
((((((...((((......))))))))))
>>__'NMR_STRUCTURE_OF_A_SYNTHETIC_SMALL_MOLECULE,_RBT203,_BOUND_TO_HIV-1_TAR_RNA_'_(PDB_00756)
GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
((((((...((((......))))))))))
>>__'NMR_STRUCTURE_OF_A_SYNTHETIC_SMALL_MOLECULE,_RBT158,_BOUND_TO_HIV-1_TAR_RNA_'_(PDB_00757)
GGCAGAUCUGAGCCUGGGAGCUCUCUGCC
((((((...((((......))))))))))
>>__'THE_STRUCTURAL_BASIS_FOR_RNA_SPECIFICITY_AND_CA2_INHIBITION_OF_AN_RNA-DEPENDENT_RNA_POLYMERASE_PHI6P2_CA2+_INHIBITION_COMPLEX_'_(PDB_00759)
UUCCUUCCUUCCGGGGGG
..((..[[..{{))]]}}
>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_EDTA_SOLUTION_'_(PDB_00760)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_AND_MN2+_BOUND_'_(PDB_00761)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_BA2+_SOLUTION_'_(PDB_00762)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_IMIDAZOLE_AND_SR2+_SOLUTION_'_(PDB_00763)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_THE_WILD_TYPE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_IN_EDTA_SOLUTION_'_(PDB_00764)
GGCCGGCAUGGUCCCAGCCUCCUCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGCGAAUGGGAC
(((((((....[[[[[(((.[[...))))))))))]]...(((((..........)))))....]]]]].
>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRODUCT_WITH_C75U_MUTAION,_CLEAVED_IN_IMIDAZOLE_AND_MG2+_SOLUTIONS_'_(PDB_00765)
GGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_THE_HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR,_WITH_C75U_MUTAION,_IN_SR2+_SOLUTION_'_(PDB_00766)
AUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
..(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_TRNA_NUCLEOTIDYLTRANSFERASE_COMPLEXED_WITH_A_PRIMER_TRNA_AND_AN_INCOMING_ATP_ANALOG_'_(PDB_00767)
GGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCGGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCACCAA
(((((((.(((.........))).)))))))(((((((.(((.........))).))))))).....
>>__'SOLUTION_STRUCTURE_OF_AN_RNA_STEM-LOOP_DERIVED_FROM_THE_3\'_CONSERVED_REGION_OF_EEL_LINE_UNAL2_'_(PDB_00798)
GGCUUUGGAUAAAAGCC
(((((((...)))))))
>>__'SOLUTION_STRUCTURE_OF_THE_EXTENDED_U6_ISL_AS_OBSERVED_IN_THE_U2/U6_COMPLEX_FROM_SACCHAROMYCES_CEREVISIAE_'_(PDB_00809)
GAGCAGUUCCCCUGCAUAAGGAUGAACCGUUC
((((((((((((((...))))).)))))))))
>>__'THE_STRUCTURE_OF_A_RIGOROUSLY_CONSERVED_RNA_ELEMENT_WITHIN_THE_SARS_VIRUS_GENOME_'_(PDB_00810)
GGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU
..((((((((...(((((((((...)))..)).))))..))))))))
>>__'HIV-1_SUBTYPE_F_GENOMIC_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00816)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'HIV-1_SUBTYPE_B_GENOMIC_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00817)
CUUGCUGAAGCGCGCACGGCAAGCUUGCUGAAGCGCGCACGGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'HIV-1_SUBTYPE_A_GENOMIC_RNA_DIMERIZATION_INITIATION_SITE_'_(PDB_00818)
CUUGCUGAGGUGCACACAGCAAGCUUGCUGAGGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'SOLUTION_STRUCTURE_OF_AUCGCA_LOOP_'_(PDB_00825)
GGAGAUCGCACUCCA
(((((....))))).
>>__'A-RIBOSWITCH-ADENINE_COMPLEX_'_(PDB_00828)
CGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUG
(((((((((...(((((((.[[[.[[)))))))........((((((]]..]]]))))))..)))))))))
>>__'G-RIBOSWITCH-GUANINE_COMPLEX_'_(PDB_00829)
GGAUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGGUC
.(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..)))))))
>>__'HIV-1_DIS_RNA_SUBTYPE_F-_MN_SOAKED_'_(PDB_00831)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'HIV-1_DIS_RNA_SUBTYPE_F-_MPD_FORM_'_(PDB_00832)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'SOLUTION_STRUCTURE_OF_THE_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_20_LOWEST_ENERGY_STRUCTURES_'_(PDB_00842)
AGUGGCGCCGACCACUUAAAAACACCGG
(((((..[[[.))))).........]]]
>>__'SOLUTION_STRUCTURE_OF_THE_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_REGULARIZED_AVERAGE_STRUCTURE_'_(PDB_00843)
AGUGGCGCCGACCACUUAAAAACACCGG
(((((..[[[.))))).........]]]
>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00855)
GGAUAUAUGAUACAAUUUGAUCAGUAUAUCC
((((((.((((........))))..))))))
>>__'SOLUTION_STRUCTURE_OF_THE_P2B-P3_PSEUDOKNOT_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00857)
GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA
[[[[[[........(((((((((]]]]]]........))))))))).
>>__'SOLUTION_STRUCTURE_OF_THE_VS_RIBOZYME_STEM-LOOP_V_IN_THE_PRESENCE_OF_MGCL2_'_(PDB_00858)
GCGAGUUGACUACUCGC
((((((.....))))))
>>__'SOLUTION_STRUCTURE_OF_THE_NEUROSPORA_VS_RIBOZYME_STEM-LOOP_V_IN_THE_PRESENCE_OF_MGCL2_WITH_MODELING_OF_BOUND_MANGANESE_IONS_'_(PDB_00859)
GCGAGUUGACUACUCGC
((((((.....))))))
>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00860)
GGAUAUAUGAUACAAUUUGAUCAGUAUAUCC
(((((((((((........)))).)))))))
>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00861)
GGAUAUAUGAUAUAAUUUGAUCAGUAUAUCC
((((((.((((........))))..))))))
>>__'NMR_STRUCTURE_OF_THE_APOB_MRNA_STEM-LOOP_AND_ITS_INTERACTION_WITH_THE_C_TO_U_EDITING_APOBEC1_COMPLEMENTARY_FACTOR_'_(PDB_00862)
GGAUAUAUGAUAUAAUUUGAUCAGUAUAUCC
((((((.((((........))))..))))))
>>__'SOLUTION_STRUCTURE_OF_THE_CENTRAL_REGION_OF_THE_HUMAN_GLUR-_B_R/G_PRE-MRNA_'_(PDB_00865)
GGUAACAAUAUGCUAAAUGUUGUUACC
((((((((((((...))))))))))))
>>__'STRUCTURAL_BASIS_FOR_RECOGNITION_OF_UUUOH_3\'-TERMINII_OF_NASCENT_RNA_POL_III_TRANSCRIPTS_BY_LA_AUTOANTIGEN_'_(PDB_00867)
UGCUGUUUUUGCUGUUUU
.((.((....)).))...
>>__'RO_AUTOANTIGEN_COMPLEXED_WITH_RNAS_'_(PDB_00868)
GCUGGUCCGAUUGACUAGCCGCUGGUCCGAUUGACUAGCCUCCGAGGUCCGA
(((((((.....))))))).(((((((.....))))))).............
>>__'HIV-1_DIS_RNA_SUBTYPE_F-_ZN_SOAKED_'_(PDB_00869)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'3\'-END_SPECIFIC_RECOGNITION_OF_HISTONE_MRNA_STEM-LOOP_BY_3\'-_EXONUCLEASE_'_(PDB_00883)
GGCUCUUUUCAGAGCCGGCUCUUUUCAGAGCCAAAA
((((((....))))))((((((....))))))....
>>__'SOLUTION_STRUCTURE_OF_BIV_TAR_HAIRPIN_COMPLEXED_TO_JDV_TAT_ARGININE-RICH_MOTIF_'_(PDB_00884)
GGCUCGUGUAGCUCAUUAGCUCCGAGCC
.(((((...((((....)))).))))).
>>__'HIV-1_DIS_RNA_SUBTYPE_F-_MONOCLINIC_FORM_'_(PDB_00886)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'MS2_COAT_PROTEIN/RNA_COMPLEX_'_(PDB_00887)
UGAGGAUCACCCAUGAGGAUCACCCA
((.((....))))((.((....))))
>>__'RNA_BACTERIOPHAGE_MS2_COAT_PROTEIN/RNA_COMPLEX_'_(PDB_00888)
AUGAGGAUUACCCAUGUGAGGAUUACCCA
(((.((....))))).((.((....))))
>>__'STRUCTURE_OF_BACTERIOPHAGE_COAT_PROTEIN-LOOP_RNA_COMPLEX_'_(PDB_00889)
GGAUCACCGGAUCACC
((....))((....))
>>__'STRUCTURE_OF_BACTERIOPHAGE_COAT_PROTEIN-LOOP_RNA_COMPLEX_'_(PDB_00890)
ACAUGAGGAUCACCCAUGUACAUGAGGAUCACCCAUGU
(((((.((....)))))))(((((.((....)))))))
>>__'CONFORMATIONAL_CHANGE_OF_PSEUDOURIDINE_55_SYNTHASE_UPON_ITS_ASSOCIATION_WITH_RNA_SUBSTRATE_'_(PDB_00891)
GGCCACGGUUCGAAUCCGUGGCGGCCACGGUUCGAAUCCGUGGC
((((((((.......))))))))(((((((.......)))))))
>>__'STRUCTURAL_BASIS_FOR_RECOGNITION_OF_UUUOH_3\'-TERMINII_OF_NASCENT_RNA_POL_III_TRANSCRIPTS_BY_LA_AUTOANTIGEN_'_(PDB_00896)
UGCUGUUUUUGCUGUUUU
.((.((....)).))...
>>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_TO_GLUTAMINE_AND_2\'DEOXY_A76_GLUTAMINE_TRNA_'_(PDB_00901)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
>>__'COUPLING_OF_ACTIVE_SITE_MOTIONS_AND_RNA_BINDING_'_(PDB_00902)
GGCAACGGUUCGAUCCCGUUGC
.(((((((.......)))))))
>>__'IF2,_IF1,_AND_TRNA_FITTED_TO_CRYO-EM_DATA_OF_E._COLI_70S_INITIATION_COMPLEX_'_(PDB_00903)
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA
(((((((..((((........))))((((((.......))))))....(((((.......))))))))))))....
>>__'RNA_STEMLOOP_FROM_BACTERIOPHAGE_QBETA_COMPLEXED_WITH_AN_N87S_MUTANT_MS2_CAPSID_'_(PDB_00905)
UGUCUAAGACAG
((((...)))).
>>__'CRYSTAL_STRUCTURE_OF_A_LUTEOVIRAL_RNA_PSEUDOKNOT_AND_MODEL_FOR_A_MINIMAL_RIBOSOMAL_FRAMESHIFTING_MOTIF_'_(PDB_00918)
GCGGCACCGUCCGCUCAAACAAACGG
((((..[[[.)))).........]]]
>>__'TAR_RNA_RECOGNITION_BY_A_CYCLIC_PEPTIDOMIMETIC_OF_TAT_PROTEIN_'_(PDB_00921)
GGCUCGUGUAGCUCAUUAGCUCCGAGCC
((((((...((((....)))).))))))
>>__'DISSECTING_THE_ROLES_OF_A_STRICTLY_CONSERVED_TYROSINE_IN_SUBSTRATE_RECOGNITION_AND_CATALYSIS_BY_PSEUDOURIDINE_55_SYNTHASE_'_(PDB_00923)
CCACGGUUCGAAUCCGUGGC
((((((.......)))))).
>>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_00926)
GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCA
((.((((..(((((.....)))))...((((.....)))).......(((((.......))))))))).)).
>>__'CRYSTAL_STRUCTURE_(I)_OF_NOVA-1_KH1/KH2_DOMAIN_TANDEM_WITH_25_NT_RNA_HAIRPIN_'_(PDB_00927)
CGCGGAUCAGUCACCCAAGCGCG
((((((.........))))))..
>>__'CRYSTAL_STRUCTURE_(II)_OF_NOVA-1_KH1/KH2_DOMAIN_TANDEM_WITH_25NT_RNA_HAIRPIN_'_(PDB_00928)
CUCGCGGAUCAGUCACCCAAGCGAG
((((((((.........))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_C27A_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_20_LOWEST_ENERGY_STRUCTURES_'_(PDB_00930)
AGUGGCGCCGACCACUUAAAAACAACGG
(((((..[[[.))))).........]]]
>>__'SOLUTION_STRUCTURE_OF_THE_C27A_SCYLV_P1-P2_FRAMESHIFTING_PSEUDOKNOT,_AVERAGE_STRUCTURE_'_(PDB_00931)
AGUGGCGCCGACCACUUAAAAACAACGG
(((((..[[[.))))).........]]]
>>__'RNA_STEMLOOP_OPERATOR_FROM_BACTERIOPHAGE_QBETA_COMPLEXED_WITH_AN_N87S,E89K_MUTANT_MS2_CAPSID_'_(PDB_00940)
GUCUAAGACAAG
(((...)))...
>>__'RNA_STEMLOOP_FROM_BACTERIOPHAGE_MS2_COMPLEXED_WITH_AN_N87S,_E89K_MUTANT_MS2_CAPSID_'_(PDB_00941)
AUGAGGAUUACCCAUGUGAGGAUUACCCAU
(((.((....))))).((.((....)))).
>>__'MS2_WILD-TYPE_RNA_STEMLOOP_COMPLEXED_WITH_AN_N87S_MUTANT_MS2_CAPSID_'_(PDB_00942)
AUGAGGAUUACCCAUGAUGAGGAUUACCCAU
(((.((....))))).(((.((....)))))
>>__'CRYSTAL_STRUCTURE_OF_STAPHYLOCOCCUS_AUREUS_TRNA_ADENOSINE_DEAMINASE,_TADA,_IN_COMPLEX_WITH_RNA_'_(PDB_00943)
UUGACUACGGAUCAAUUGACUACGGAUCAAGACUACGGUUUGACUACGGAUCAA
(((((.....)))))(((((.....))))).........(((((.....)))))
>>__'GUANINE_RIBOSWITCH_C74U_MUTANT_BOUND_TO_2,6-DIAMINOPURINE_'_(PDB_00944)
GACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUC
((((((.....(((((.[[[.[[)))))..........((((((]]..]]]))))))..))))))
>>__'COMPLETE_RNA_POLYMERASE_II-RNA_INHIBITOR_COMPLEX_'_(PDB_00945)
CAGCACUGAUUGCGGUCGAGGUAGCUUGAUG
.((((.....))))((((((....)))))).
>>__'RNA_RECOGNITION_BY_THE_VTS1_SAM_DOMAIN_'_(PDB_00948)
GGAGGCUCUGGCAGCUUUC
(((((((.....)))))))
>>__'STRUCTURE_OF_THE_SMAUG_RECOGNITION_RNA_ELEMENT_'_(PDB_00949)
GGAGGCUCUGGCAGCUUUC
(((((((.....)))))))
>>__'STRUCTURE_OF_HIV-1(LAI)_GENOMIC_RNA_DIS_'_(PDB_00950)
CUUGCUGAAGCGCGCACGGCAAGCUUGCUGAAGCGCGCACGGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'STRUCTURE_OF_HIV-1(MAL)_GENOMIC_RNA_DIS_'_(PDB_00951)
CUUGCUGAGGUGCACACAGCAAGCUUGCUGAGGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'CRYSTAL_STRUCTURE_OF_E._COLI_5-METHYLURIDINE_METHYLTRANSFERASE_RUMA_IN_COMPLEX_WITH_RIBOSOMAL_RNA_SUBSTRATE_AND_S-ADENOSYLHOMOCYSTEINE._'_(PDB_00961)
AGCGAAAUUCCUUGUCGGGUAAGUUCCGACAGCGAAAUUCCUUGUCGGGUAAGUUCCGAC
.............(((((.......))))).............(((((.......)))))
>>__'MS2_(N87A_MUTANT)-_RNA_HAIRPIN_COMPLEX_'_(PDB_00963)
AUGAGGAUUACCCAUUGAGGAUUACCCA
(((.((....)))))((.((....))))
>>__'MS2_(N87AE89K_MUTANT)-_RNA_HAIRPIN_COMPLEX_'_(PDB_00964)
ACAUGAGGAUUACCCAUGUCAUGAGGAUUACCCAUG
(((((.((....)))))))..((.........))..
>>__'MS2_(N87AE89K_MUTANT)-_VARIANT_QBETA_RNA_HAIRPIN_COMPLEX_'_(PDB_00965)
UGUCUAAGACUGGUCUAAGAC
.(((...)))..(((...)))
>>__'MS2_(N87AE89K_MUTANT)-_QBETA_RNA_HAIRPIN_COMPLEX_'_(PDB_00966)
UGUCUAAGACAGUGUCUAAGACA
.(((...)))..((((...))))
>>__'MS2-RNA_HAIRPIN_(5BRU-5)_COMPLEX_'_(PDB_00968)
CAUGAGGAUUACCCAUGCAUGAGGAUUACCCAUG
((((.((....))))))((((.((....))))))
>>__'MS2-RNA_HAIRPIN_(2ONE-5)_COMPLEX_VIRUS_'_(PDB_00970)
CAUGAGGAUUACCCAUGCAUGAGGAUUACCCAUG
((((.((....))))))..((.((....))))..
>>__'MS2-RNA_HAIRPIN_(2THIOURACIL-5)_COMPLEX_'_(PDB_00971)
CAUGAGGAUUACCCAUGUGAGGAUUACCCA
((((.((....))))))((.((....))))
>>__'MS2-RNA_HAIRPIN_(2SU-5-6)_COMPLEX_'_(PDB_00972)
CAUGAGGAUUACCCAUGUGAGGAUUACCCA
((((.........))))((.........))
>>__'MS2-RNA_HAIRPIN_(A-5)_COMPLEX_'_(PDB_00973)
AUGAGGAUAACCCAUGAGGAUAACCCA
.((.((....))))((.((....))))
>>__'MS2-RNA_HAIRPIN_(G-5)_COMPLEX_'_(PDB_00974)
AUGAGGAUGACCCAUUGAGGAUGACCCA
(((.((....)))))((.((....))))
>>__'REFINEMENT_OF_P4_STEMLOOP_STRUCTURE_USING_RESIDUAL_DIPOLAR_COUPLING_DATA_'_(PDB_00975)
GGAAGUCCGGUCUUCGGACCGGCUUCC
.((((.(((((......))))))))).
>>__'REFINEMENT_OF_RNASE_P_P4_STEMLOOP_STRUCTURE_USING_RESIDUAL_DIPOLAR_COUPLINGS-_COBALT(III)_HEXAMMINE_COMPLEX_STRUCTURE_'_(PDB_00977)
GGAAGUCCGGUCUUCGGACCGGCUUCC
(((((.(((((......))))))))))
>>__'SOLUTION_RNA_STRUCTURE_OF_LOOP_REGION_OF_THE_HIV-1_DIMERIZATION_INITIATION_SITE_IN_THE_KISSING-LOOP_DIMER_'_(PDB_00988)
GCUGAAGUGCACACGGCGCUGAAGUGCACACGGC
((((..[[[[[[.))))((((..]]]]]].))))
>>__'SOLUTION_RNA_STRUCTURE_MODEL_OF_THE_HIV-1_DIMERIZATION_INITIATION_SITE_IN_THE_KISSING-LOOP_DIMER_'_(PDB_00990)
GGGUCGGCUUGCUGAAGUGCACACGGCAAGAGGCGACCCGGGUCGGCUUGCUGAAGUGCACACGGCAAGAGGCGACCC
(((((((((((((((.[[[[[[)))))))))..))))))((((((((((((((..]]]]]].))))))))..))))))
>>__'COCRYSTAL_STRUCTURE_OF_AN_RNA_SULFURATION_ENZYME_MNMA_AND_TRNA-GLU_IN_THE_PRE-REACTION_STATE_'_(PDB_00999)
GUCCCCUUCGUCUAGAGGCCCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGGG
..((.....(((((.......)))))(((((((.....)))))))....((((.......))))...)).
>>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_01002)
GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCACCA
(((((((....(((.....)))...((((((.....)))))).....(((((.......))))))))))))....
>>__'COMPLEX_STRUCTURE_OF_CCA_ADDING_ENZYME_WITH_MINI-HELIX_LACKING_CCA_'_(PDB_01003)
GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCA
(((((((..(((.......)))..))))))).
>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDC_'_(PDB_01004)
GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCAC
((((((((((((.......))))))))))))..
>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDC_AND_CTP_'_(PDB_01005)
GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCAC
((((((((((((.......))))))))))))..
>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDCC_'_(PDB_01006)
GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACC
((((((((((((.......))))))))))))...
>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINIDCC_AND_ATP_'_(PDB_01007)
GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACC
((((((((((((.......))))))))))))...
>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME_WITH_TRNAMINICCA_'_(PDB_01008)
GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACCA
((((((((((((.......))))))))))))....
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_AND_O-PHOSPHOSERINE_'_(PDB_01009)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
((((((([[(((]].......)))..((((.......))))......(((((.......))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_'_(PDB_01010)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
..((((([[(((]].......)))..(((((.....)))))......(((((.......))))))))))..
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAOPAL_AND_O-PHOSPHOSERINE_("OPAL_COMPLEX")_'_(PDB_01011)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUUCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAAMBER_AND_O-PHOSPHOSERINE_("AMBER_COMPLEX")_'_(PDB_01012)
GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUCUAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC
(((((((..(((.........))).(((((.......))))).....(((((.......))))))))))))
>>__'COMPLEX_STRUCTURE_OF_CCA-ADDING_ENZYME,_MINI-DCC_AND_CTP_'_(PDB_01013)
GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCACC
((((((((((((.......))))))))))))...
>>__'GUANINE_RIBOSWITCH_A21U,_U75A_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01020)
GGACAUUUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACAAUGUCCA
.((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))..
>>__'GUANINE_RIBOSWITCH_A21G,_U75C_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01021)
GGACAUGUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACCAUGUCCA
.((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))..
>>__'GUANINE_RIBOSWITCH_U22A,_A52U_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01022)
GGACAUAAAAUCGCGUGGAUAUGGCACGCAAGUUUCUUCCGGGCACCGUAAAUGUCCGACUAUGUCCA
(((((((.....(((((.[[..[[)))))..........((((((]]...]]))))))..))))))).
>>__'GUANINE_RIBOSWITCH_U22C,_A52G_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01023)
GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCA
(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))).
>>__'GUANINE_RIBOSWITCH_U47C_MUTANT_BOUND_TO_HYPOXANTHINE_'_(PDB_01024)
GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGCUUCUACCGGGCACCGUAAAUGUCCGACUAUGUCCA
(((((((.....(((((.[[..[[)))))..........((((((]]...]]))))))..))))))).
>>__'STRUCTURE_OF_THE_SRE_RNA_'_(PDB_01025)
GGAGAGGCUCUGGCAGCUUUUCC
(((((((((.....)))))))))
>>__'STRUCTURE_OF_THE_SAM_DOMAIN_OF_VTS1P_IN_COMPLEX_WITH_RNA_'_(PDB_01026)
GGAGAGGCUCUGGCAGCUUUUCC
(((((((((.....)))))))))
>>__'NMR_SOLUTION_OF_HIV-1_LAI_KISSING_COMPLEX_'_(PDB_01040)
GGUUGCUGAAGCGCGCACGGCAACGGUUGCUGAAGCGCGCACGGCAAC
.(((((((..[[[[[[.))))))).(((((((..]]]]]].)))))))
>>__'SOLUTION_NMR_STRUCTURE_OF_DOMAIN_5_FROM_THE_PYAIELLA_LITTORALIS_(PL)_GROUP_II_INTRON_'_(PDB_01042)
GAGCCGUGUGCGAUGAAAGUCGCAAGCACGGUUC
((((((((.(((((....)))))...))))))))
>>__'CRYSTAL_STRUCTURE_OF_AA-AGO_WITH_EXTERNALLY-BOUND_SIRNA_'_(PDB_01044)
AGACAGCAUAUAUGCUGUCUUUAGACAGCAUAUAUGCUGUCUUU
.((((((((((.((((((......)))))).))))))))))...
>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_NEAMINE_'_(PDB_01046)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_NEOMYCIN_'_(PDB_01047)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_RIBOSTAMYCIN_'_(PDB_01048)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'HIV-1_DIS_KISSING-LOOP_IN_COMPLEX_WITH_LIVIDOMYCIN_'_(PDB_01049)
CUUGCUGAAGUGCACACAGCAAGCUUGCUGAAGUGCACACAGCAAG
(((((((..[[[[[[.)))))))(((((((..]]]]]].)))))))
>>__'SOLUTION_STRUCTURE_OF_A_CONSERVED_RNA_HAIRPIN_OF_EEL_LINE_UNAL2_'_(PDB_01050)
GGUUGUACGUCGCUUUGGAUAAAAGCGUCUGCGACC
((((((..(((((((.......))))))).))))))
>>__'THE_STRUCTURE_OF_STEM_LOOP_IV_OF_TETRAHYMENA_TELOMERASE_RNA_'_(PDB_01051)
GAGACUAUCGACAUUUGAUACACUAUUUAUCAAUGGAUGUCUC
(((((......(((..(((((.....))))).)))...)))))
>>__'CRYSTAL_STRUCTURE_OF_RNASE_Z/TRNA(THR)_COMPLEX_'_(PDB_01053)
GCUUCCAUAGCUCAGCAGGUAGAGCGUCAGCGGUUCGAGCCCGCUUGGAAGCU
(((((((..((((........))))...(((((.......)))))))))))).
>>__'SOLUTION_STRUCTURE_OF_THE_HELIX_II_TEMPLATE_BOUNDARY_ELEMENT_FROM_TETRAHYMENA_TELOMERASE_RNA_'_(PDB_01056)
GGCAGAUCUGUAAUAGAACUGCC
(((((((((.....)))))))))
>>__'A_DUAL_MODE_OF_RNA_RECOGNITION_BY_THE_RBMY_PROTEIN_'_(PDB_01057)
GGACUGUCCACAAGACAGUCC
((((((((.....))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_ANTICODON_LOOP_OF_S._POMBE_TRNAI_INCLUDING_THE_NATURALLY_OCCURRING_N6-THREONYL_ADENINE_'_(PDB_01058)
ACGGGCUCAUAACCCGU
(((((((...)))))))
>>__'NMR_STRUCTURE_OF_THE_AQUIFEX_AEOLICUS_TMRNA_PSEUDOKNOT_PK1_'_(PDB_01059)
GGGGUGGCUCCCCUAACAGCCG
((((.[[[.)))).....]]].
>>__'MODIFIED_PYRIMIDINES_SPECIFICALLY_BIND_THE_PURINE_RIBOSWITCH_'_(PDB_01066)
GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUCCU
(((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))).
>>__'RNA_RECOGNITION_AND_CLEAVAGE_BY_AN_SPLICING_ENDONUCLEASE_'_(PDB_01074)
GCGACCGACCAUAGCUGCUGCAGCGGUCAAAGGUCGCGCGACCGACCAUAGCUGCAUGCAGCGGUCAAAGGUCGC
.(((((((((...((((...))))))))...))))).((((((((((...((........))))))...))))))
>>__'TRANSLOCATION_OF_A_TRNA_WITH_AN_EXTENDED_ANTICODON_THROUGH_THE_RIBOSOME_'_(PDB_01084)
GGCCAGACUCCCGAAUCUGGCC
(((((((........)))))))
>>__'SOLUTION_STRUCTURE_OF_A_PURINE_RICH_HEXALOOP_HAIRPIN_BELONGING_TO_PGY/MDR1_MRNA_AND_TARGETED_BY_ANTISENSE_OLIGONUCLEOTIDES_'_(PDB_01086)
GAGGUCGGGAUGGAUCUC
((((((......))))))
>>__'SOLUTION_STRUCTURE_OF_THE_TETRAHYMENA_TELOMERASE_RNA_STEM_IV_TERMINAL_LOOP_'_(PDB_01097)
GGCGAUACACUAUUUAUCGCC
((((((((.....))))))))
>>__'STRUCTURE_OF_THE_AAGU_TETRALOOP_'_(PDB_01108)
GGCGUGAUCAAGUGAUCGCGCC
(((((((((....)))))))))
>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_PYROPHOSPHATE,_MANGANESE_IONS_'_(PDB_01111)
GCGACUCGGGGUGCCCUCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUGCCAGCGAGGGAAGUCGCA
((((((((((((((((......))))......)))))).(((((((.((((......))))))))))))))))).
>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_PYROPHOSPHATE,_CALCIUM_IONS_'_(PDB_01112)
GCGACUCGGGGUGCCCUGCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUCCAGCGAGGGAAGUCGCA
((((((((((((((((.......))))......)))))).(((((((.((((.....))))))))))))))))).
>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_PYROPHOSPHATE,_BARIUM_IONS_'_(PDB_01113)
GCGACUCGGGGUGCCCUCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUGCCAGCGAGGGAAGUCGCA
((((((((((((((((......))))......)))))).(((((((.((((......))))))))))))))))).
>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_THIAMINE_MONOPHOSPHATE_'_(PDB_01114)
GCGACUCGGGGUGCCCUGCGUGAAGGCUGAGAAAACCCGUAACCUGAUCUGGAUAAUGCCAGCGAGGGAAGUCGCA
((((((((((((((((.......))))......)))))).(((((((.((((......))))))))))))))))).
>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_BENFOTIAMINE_'_(PDB_01115)
GCGACUCGGGGUGCCCUGCAAGGCUGAGAAAACCCGUAUACCUGACUGGAUAAUGCCAGCGUAGGGAAGUCGCA
((((((((((((((((....))))......))))))...((((((((((......)))))).)))).)))))).
>>__'CRYSTAL_STRUCTURE_OF_AN_E._COLI_THI-BOX_RIBOSWITCH_BOUND_TO_PYRITHIAMINE_'_(PDB_01116)
GCGACUCGGGGUGCCCGCGUAAGGCUGAGAAAACCCGUAACCUGAUGGAUAAUCCAGAGGGAAGUCGCA
((((((((((((((((.....))))......)))))).(((((..............))))))))))).
>>__'CRYSTAL_STRUCTURE_OF_AN_H/ACA_BOX_RNP_FROM_PYROCOCCUS_FURIOSUS_'_(PDB_01118)
GGGUCCGCCUUGAUGCCCGGGUGAAAGCAUGAUCCCGGGUAAUAUGGCGGACCCACA
(((((((((.....((((((((((......)))))))))).....)))))))))...
>>__'CRYSTAL_STRUCTURE_OF_PSEUDOURIDINE_SYNTHASE_RLUA:_INDIRECT_SEQUENCE_READOUT_THROUGH_PROTEIN-INDUCED_RNA_STRUCTURE_'_(PDB_01126)
GAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAAUCCCCUCGAGGGGAUGAAAUCCCCUC
(((((((......)))))))(((((((......)))))))(((((((......)))))))(((((((.....)))))))
>>__'CRYSTAL_STRUCTURE_OF_IRON_REGULATORY_PROTEIN_1_IN_COMPLEX_WITH_FERRITIN_H_IRE-RNA_'_(PDB_01130)
GUUCUUGCUUCAACAGUGUUUGAACGGAACGUUCUUGCUUCAACAGUGUUUGAACGGAAC
(((((...(((((......))))).)))))(((((...(((((......))))).)))))
>>__'SOLUTION_STRUCTURE_OF_THE_APICAL_STEM-LOOP_OF_THE_HUMAN_HEPATITIS_B_VIRUS_ENCAPSIDATION_SIGNAL_'_(PDB_01133)
GGCCUCCAAGCUGUGCCUUGGGUGGCC
((((((((((......)))))).))))
>>__'PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_TRNA_AND_A_PHENYLALANYL-ADENYLATE_ANALOG_'_(PDB_01134)
GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA
(((((((....((........))...((((((.....)))))).....((((.........)))))))))))....
>>__'MS2-RNA_HAIRPIN_(C-7)_COMPLEX_'_(PDB_01135)
AUGAGGCUCACCCAUGUGAGGCUCACCCA
(((.((....))))).((.((....))))
>>__'MS2-RNA_HAIRPIN_(4ONE-5)_COMPLEX_'_(PDB_01136)
AUGAGGAUUACCCAUAUGAGGAUUACCCAU
.((.((....))))..((.((....)))).
>>__'MS2-RNA_HAIRPIN_(C-10)_COMPLEX_'_(PDB_01137)
UGCGGAUCACCCAUGCGGAUCACCCA
((.((....))))((.((....))))
>>__'MS2-RNA_HAIRPIN_(G-10)_COMPLEX_'_(PDB_01138)
AUCGCGAUUACGGAUCGCGAUUACGG
(((.((....)))))..((....)).
>>__'STRUCTURAL_BASIS_OF_RSMA/CSRA_RNA_RECOGNITION:_STRUCTURE_OF_RSME_BOUND_TO_THE_SHINE-DALGARNO_SEQUENCE_OF_HCNA_MRNA_'_(PDB_01145)
GGGCUUCACGGAUGAAGCCCGGGCUUCACGGAUGAAGCCC
(((((((......)))))))(((((((......)))))))
>>__'MODEL_FOR_THIOSTREPTON_BINDING_TO_THE_RIBOSOMAL_L11-RNA_'_(PDB_01146)
GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC
((((((.((..(((.........)))..)).........(((......))).))))))
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E.COLI_TRNA-VAL3_WITH_NO_MODIFICATIONS_'_(PDB_01147)
CCUCCCUUACAAGGAGG
((((((.....))))))
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E._COLI_TRNA-_VAL3_WITH_2_MODIFICATIONS_(CMO5U34_M6A37)_'_(PDB_01148)
CCUCCCUUACAAGGAGG
(((((.......)))))
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E._COLI_TRNA-_VAL3_WITH_1_MODIFICATION_(CMO5U34)_'_(PDB_01149)
CCUCCCUUACAAGGAGG
((((((.....))))))
>>__'NMR_SOLUTION_STRUCTURE_OF_THE_ANTICODON_OF_E.COLI_TRNA-VAL3_WITH_1_MODIFICATION_(M6A37)_'_(PDB_01151)
CCUCCCUUACAAGGAGG
((((((.....))))))
>>__'SOLUTION_STRUCTURE_OF_THE_FRAMESHIFT-INDUCING_RNA_STEM-LOOP_IN_SIV_'_(PDB_01152)
GGAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUCC
((((((((((((..((...)).))))))))))))
>>__'CRYSTAL_STRUCTURE_OF_RNASE_III_FROM_AQUIFEX_AEOLICUS_COMPLEXED_WITH_DS-RNA_AT_1.7-ANGSTROM_RESOLUTION_'_(PDB_01165)
AAGGUCAUUCGAGUGGCCUUGCAAGGUCAUUCGAGUGGCCUUGC
((((((((([[)))))))))..(((((((((]])))))))))..
>>__'SOLUTION_STRUCTURE_OF_U2_SNRNA_STEM_I_FROM_S._CEREVISIAE_'_(PDB_01168)
GGUUUGCCUUUUGGCUUACC
((((((((....))))))))
>>__'HEPATITIS_DELTA_VIRUS_GEMONIC_RIBOZYME_PRECURSOR_WITH_C75U_MUTATION_AND_BOUND_TO_MONOVALENT_CATION_TL+_'_(PDB_01185)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
.(((((((...[[[[[[(((.[[.....))))))))))]]...(((((..........)))))....]]]]]]
>>__'HEPATITIS_DELTA_VIRUS_RIBOZYME_PRECURSOR_STRUCTURE,_WITH_C75U_MUTATION,_BOUND_TO_TL+_AND_COBALT_HEXAMMINE_(CO(NH3)_63+)_'_(PDB_01190)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC
..((((((...[[[[[[(((.[[.....))))))))).]]...(((((..........)))))....]]]]]]
>>__'NMR_STRUCTURE_OF_A_KISSING_COMPLEX_FORMED_BETWEEN_THE_TAR_RNA_ELEMENT_OF_HIV-1_AND_A_LNA/RNA_APTAMER_'_(PDB_01194)
GGAGCCUGGGAGCUCCCACGGUCCCAGACGUG
((((([[[[[.)))))(((((.]]]]])))))
>>__'STRUCTURE_OF_A_HUMAN_PRP31-15.5K-U4_SNRNA_COMPLEX_'_(PDB_01199)
AUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAU
(((((.(((...((((.....))))))))))))(((((.(((...((((.....))))))))))))
>>__'SOLUTION_STRUCTURE_OF_AN_RRNA_SUBSTRATE_BOUND_TO_THE_PSEUDOURIDYLATION_POCKET_OF_A_BOX_H/ACA_SNORNA_'_(PDB_01202)
GGACCCGCCACUGCAGAGAUGCAAUCCAGUGGUCC
(((((......((((....)))).......)))))
>>__'STRUCTURE_OF_THE_MRNA_BINDING_FRAGMENT_OF_ELONGATION_FACTOR_SELB_IN_COMPLEX_WITH_SECIS_RNA._'_(PDB_01205)
GGCGUUGCCGGUCUGGCAACGCCGGCGUUGCCGGUCUGGCAACGCC
(((((((((.....)))))))))(((((((((.....)))))))))
>>__'NMR_STRUCTURE_OF_A_KISSING_COMPLEX_FORMED_BETWEEN_THE_TAR_RNA_ELEMENT_OF_HIV-1_AND_A_LNA_MODIFIED_APTAMER_'_(PDB_01206)
GGAGCCUGGGAGCUCCCACGGUCCCAGACGUG
((((([[[[[[)))))(((((]]]]]])))))
>>__'SOLUTION_STRUCTURE_OF_THE_CR7_TERMINAL_HAIRPIN_LOOP_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_01237)
GGAGUGCCUGAGCUGUGGCACUCC
((((((((........))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_U64_H/ACA_SNORNA_3\'_TERMINAL_HAIRPIN_LOOP_'_(PDB_01238)
GGAGUGCCUUACUGUGGCACUCC
((((((((.......))))))))
>>__'SOLUTION_STRUCTURE_OF_THE_U85_C/D-H/ACA_SCARNA_5\'_TERMINAL_HAIRPIN_LOOP_'_(PDB_01239)
GGCACAGAGUUAUGUGCC
(((((((....)))))))
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE_'_(PDB_01258)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......)))).(((((((...))))))).....(((((.......))))))))))).....
>>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMYL)-SULFAMOYL]ADENOSINE_'_(PDB_01259)
GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA
((((((..((((.......))))((((((((...))))))))....(((((.......))))))))))).....
>>__'SOLUTION_STRUCTURE_OF_THE_TOBRAMYCIN-RNA_APTAMER_COMPLEX,_NMR,_13_STRUCTURES_'_(PDB_01262)
ACUUGGUUUAGGUAAUGAGU
((((((((....))))))))
>>__'C-TERMINAL_DOMAIN(WH2-WH4)_OF_ELONGATION_FACTOR_SELB_IN_COMPLEX_WITH_SECIS_RNA_'_(PDB_01270)
GGCGUUGCCGGUCUGGCAACGCCGGCGUUGCCGGUCUGGCAACGCC
(((((((((.....)))))))))(((((((((.....)))))))))
>>__'CRYSTAL_STRUCTURE_OF_AN_ESCHERICHIA_COLI_TRNAGLY_MICROHELIX_AT_2.0_ANGSTROM_RESOLUTION_'_(PDB_01281)
GCGGGAAGCGGGAAUUCCCGCUUCCCGC
((((((([[[[[[[)))))))]]]]]]]
>>__'CRYSTAL_STRUCTURE_OF_DOMAIN_III_OF_THE_CRICKET_PARALYSIS_VIRUS_IRES_RNA_'_(PDB_01299)
GGUUAUUCAGAUUAGGUAGUCGAAUGACCUAAGAAAUUUACCU
((((((((.((..[[[[[.)))))))))).........]]]]]
>>__'5\'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3\'_'_(PDB_01313)
GAUCACUUCGGUGAUCACUUCGGU
....((((((((....))))))))
>>__'SOLUTION_STRUCTURE_OF_HIV-1_REV_PEPTIDE-RNA_APTAMER_COMPLEX_'_(PDB_01332)
GGUGUCUUGGAGUGCUGAUCGGACACC
(((((((..((.......)))))))))
>>__'MS2_PROTEIN_CAPSID/RNA_COMPLEX_'_(PDB_01337)
CCGGAGGAUCACCACGGGCGGAGGAUCACCACGG
((((.((....)))))).(((.((....))))).
>>__'F6_APTAMER_MS2_COAT_PROTEIN_COMPLEX_'_(PDB_01338)
CCACAGUCACUGGGCAGUCACUGG
((.(((...)))))(((...))).
>>__'MS2_PROTEIN_CAPSID/RNA_COMPLEX_'_(PDB_01340)
UCGCCAACAGGCGGGCCAACAGGCG
(((((....)))))(((....))).
>>_PKB1:_Bovine_Leukemia_Virus_(BLV)
AAAAAACUAAUAGAGGGGGGACUUAGCGCCCCCCAAACCGUAACCCC
..............[[[[[[.....(((]]]]]]....)))......
>>_PKB2:_Beet_Western-Yellows_Virus_(BWYV)
GGGAAACGGAGUGCGCGGCACCGUCCGCGGAACAAACGGAGAAGGCAGCU
.............[[[[[..((((]]]]]......))))...........
>>_PKB3:_Equine_Infectious_Anemic_Virus_(EIAV)
AAAAAACGGGAAGCAAGGGGCUCAAGGGAGGCCCCAGAAACAAACUUUCCCGAU
................[[[[[[...((((]]]]]]............))))...
>>_PKB4:_Feline_Immunodeficiency_Virus_(FIV)
GGGAAACUGGAAGGCGGGGCGAGCUGCAGCCCCAGUGAAUCAAAUGCAGC
...............[[[[[..((((((]]]]]...........))))))
>>_PKB5:_turnip_yellow_mosaic_virus_(TYMV)
CGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCGGAACC
...............(((....[[[[[)))...]]]]]...
>>_PKB6:_kennedya_yellow_mosaic_virus_(KYMV-BP)
GGGGUGCAACUCCCCCGUCUAUCCUGGACGUCACCAGGACCA
...............(((...[[[[[[)))...]]]]]]...
>>_PKB7:_cacao_yellow_mosaic_virus_(CaYMV)
GGUGGUGCAACUCCCCCGUCCUCCCGAACGUCAUCGGGACCA
................(((..[[[[[[)))...]]]]]]...
>>_PKB8:_physalis_mottle_virus_(PhyMV)
UGGGUGCAACUCCCCCCCCUUCCGUGGGUAACGGAAACCA
..............(((..[[[[[[)))..]]]]]]....
>>_PKB9:_desmodium_yellow_mottle_virus_(DYMV)
GGGGUGCAACUCCCCCGUCUAUCCUGGACGUCACCAGGACCA
...............(((...[[[[[[)))...]]]]]]...
>>_PKB10:_ononis_yellow_mosaic_virus_(OYMV)
UGGGUUCAACUCCCCCCCUUUUCCGAGGGUAUCGGAAACC
..............(((...[[[[[[)))..]]]]]]...
>>_PKB11:_clitoria_yellow_vein_virus_(CYVV)
UGGGUGCAACCCCCCCGUCCAUCUCGAACGUCAUCGAGACCA
...............(((...[[[[[[)))...]]]]]]...
>>_PKB12:_wild_cucumber_mosaic_virus_(WCMV)
CGGGUGCAACCCCCCCUCCCCCCGUAGGUUAACGGGACCA
..............(((...[[[[[)))...]]]]]....
>>_PKB13:_calopogonium_yellow_vein_virus_(CaYVV)
GGGGUGCGACUCCCCCGUCUAUCCUGAACGUCAUCAGGACCA
...............(((...[[[[[[)))...]]]]]]...
>>_PKB14:_andean_potato_latent_virus_(APLV)
CGGGUGCGACUCCCCCCCCUCCUGUGGGCUACAGGAACCA
..............(((..[[[[[[)))..]]]]]]....
>>_PKB15:_eggplant_mosaic_virus_(EMV)
UGGGUGCGACUCCCCCCCCUCCCGUGGGUCAACGGGAACCA
..............(((..[[[[[[)))...]]]]]]....
>>_PKB16:_okra_mosaic_virus_(OMV)
GGGGUGCAACUCCCCCGCCCAUCUCGAGCGUCAUCGAGACCA
...............(((...[[[[[[)))...]]]]]]...
>>_PKB17:_tobacco_mosaic_virus_(CcTMV)
GGGGAGCAUUACCCCCCCAAAACCCUGGGGAUACAGGGCCCA
...............(((....[[[[[)))...]]]]]....
>>_PKB18:_tobacco_mosaic_virus_(TMV)
GGGGUUCGAAUCCCCCCGUUACCCCCGGUAGGGGCCCA
...............(((...[[[[)))..]]]]....
>>_PKB19:_pepper_mild_mottle_virus_(PMMV-I)
GGGGUUCGAAUCCCCCCCGAACCGCGGGUAGCGGCCCA
...............(((...[[[[)))..]]]]....
>>_PKB20:_cucumber_green_mottle_mosaic_virus_(CGMMV)
GGGGUUCGAAUCCCCCCUUUUCCCCGGGUAGGGGCCCA
...............(((...[[[[)))..]]]]....
>>_PKB21:_tobacco_mosaic_virus_(TMV-L)
GGGAUUCGAAUUCCCCCGGAACCCCCGGUUGGGGCCCA
...............(((...[[[[)))..]]]]....
>>_PKB22:_satellite_tobacco_mosaic_virus_(STMV)
GGGGUUCGAAUCCCUCCCUAACCGCGGGUAAGCGGCCCA
...............(((...[[[[)))...]]]]....
>>_PKB23:_tobacco_mild_green_mosaic_virus_(TMGMV)
GAGGUUCGAAUCCUCCCGUAACCGCCGGUAGCGGCCCA
...............(((...[[[[)))..]]]]....
>>_PKB24:_paprika_mild_mottle_virus_(PaMMV)
GGGGUUCGAAUCCCCCCUUUACCCCGGGUAUGGGGCCCA
...............(((...[[[[)))...]]]]....
>>_PKB25:_turnip_vein-clearing_virus_(TVCV)
GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
...............(((..[[[[)))..]]]]....
>>_PKB26:_oilseed_rape_mosaic_virus_(ORMV)
GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
...............(((..[[[[)))..]]]]....
>>_PKB27:_pepper_mild_mottle_virus_(PMMV-S)
GGGGUUCGAAUCCCCCCCGAACCGCGGGUAGCGGCCCA
...............(((...[[[[)))..]]]]....
>>_PKB28:_odontoglossum_ringspot_virus_(ORSV-S1)
GGGAUUCGAAUUCCCCCUUACCUCGGGUAGAGGCCCA
...............(((..[[[[)))..]]]]....
>>_PKB29:_tobacco_mosaic_virus_(TMVcg)
GAGGUUCGAAUCCUCCCUAACCCCGGGUAGGGGCCCA
...............(((..[[[[)))..]]]]....
>>_PKB30:_soil-borne_wheat_mosaic_virus_(SBWMV1)
GGGGUUCAAAUCCCCCCCGAACCGGAGGGUUAUCCGGCCCA
...............(((...[[[[[)))...]]]]]....
>>_PKB31:_soil-borne_wheat_mosaic_virus_(SBWMV2)
GGGGUUCAAUUCCCCCCCCAUCCGGAGGGUUAUCCGGCCC
...............(((...[[[[[)))...]]]]]...
>>_PKB32:_potato_mop-top_virus_(PMTV2)
GGGUGCAACUCCCCCCCCCUUGGAGGGUAUCCAAGACC
.............(((..[[[[[[)))..]]]]]]...
>>_PKB33:_peanut_clump_virus_(PCV1)
GGUGCAAAUCCCCCGCUGAAACGGAGCGAUAUCCGUCCCA
.............(((....[[[[[)))...]]]]]....
>>_PKB34:_peanut_clump_virus_(PCV2)
GGUGCAAAUCCCCCGCUGAAACGGAGCGAUAUCCGUCCCA
.............(((....[[[[[)))...]]]]]....
>>_PKB35:_Indian_peanut_clump_virus_(IPCV1)
GGUGCAAAUCCCCCGCCGAUACGGAGCGAUAUCCGUCCCA
.............(((....[[[[[)))...]]]]]....
>>_PKB36:_beet_soil-borne_virus_(BSBV1)
GGGGUGCAAAUCCCCCCCUUUACUUGAGGGAAAUCAAGCCC
...............(((....[[[[[)))...]]]]]...
>>_PKB37:_beet_soil-borne_virus_(BSBV2)
GGGGUGCAAAUCCCCCCCUUAACUUGAGGGAAAUCAAGCCC
...............(((....[[[[[)))...]]]]]...
>>_PKB38:_beet_soil-borne_virus_(BSBV3)
GGGGUGCAACUCCCCCCCUUAACUAGAGGGAAAUCUAGCCC
...............(((....[[[[[)))...]]]]]...
>>_PKB39:_beet_virus_Q_(BVQ1)
GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCCC
...............(((...[[[[[)))...]]]]]....
>>_PKB40:_beet_virus_Q_(BVQ2)
GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCC
...............(((...[[[[[)))...]]]]]...
>>_PKB41:_beet_virus_Q_(BVQ3)
GGGGUGCAAAUCCCCCCCUAACUUGAGGGAAAUCAAGCCCC
...............(((...[[[[[)))...]]]]]....
>>_PKB42:_potato_leafroll_virus_(PLRV-W)
UUUAAAUGGGCGAGCGGCACCGCCCGCCAAAACAAACGG
.............((((..[[[.)))).........]]]
>>_PKB43:_potato_leafroll_virus_(PLRV-S)
UUUAAAUGGGCAAGCGGCACCGUCCGCCAAAACAAACGG
.............((((..[[[[))))........]]]]
>>_PKB44:_cucurbit_aphid-borne_yellows_virus_(CABYV)
GGGAAACGGGCAGGCGGCGGCGACCGCCGAAACAACCGC
............(((((..[[[.)))))........]]]
>>_PKB45:_pea_enation_mosaic_virus_(PEMV)
GGGAAACGGAUUAUUCCGGUCGACUCCGGAGAAACAAAGUC
.............((((((..[[[[))))))......]]]]
>>_PKB46:_barley_yellow_dwarf_virus_(BYDV-NY-RPV)
GGGAAACGGGAAGGCGGCGGCGUCCGCCGUAACAAACGC
............(((((..[[[[))))).......]]]]
>>_PKB47:_Moloney_murine_leukemia_virus_(Mo-MuLV)
UAGGGAGGUCAGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGC
...........((((((((.[[[[[[[)))).))))..................]]]]]]]
>>_PKB48:_spleen_necrosis_virus_(SNV)
UAGGGCCGUCAGGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC
...........((((((.(..[[[[[[[).))))))..................]]]]]]]
>>_PKB49:_E.coli_(Ec_PK1)
CGAGGGGCGGUUGGCCUCGUAAAAAGCCGC
(((((.[[[[[[..))))).....]]]]]]
>>_PKB50:_E.coli_(Ec_PK2)
CCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAG
(((((((((((..(((...[[[[[)))..))))....)))))))..........]]]]]
>>_PKB51:_E.coli_(Ec_PK3)
GCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGC
((((...(((((.[[[[[)))))...))))...........]]]]]
>>_PKB52:_E.coli_(Ec_PK4)
GUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC
((((((((((.(((.[[[.[[[))).)))))))))).........]]].]]]
>>_PKB53:_tobacco_mosaic_virus_(TMV_UPD-PK1)
ACGGAUUGUGUCCGUAAUCACA
..(((.[[[[))).....]]]]
>>_PKB54:_tobacco_mosaic_virus_(TMV_UPD-PK2)
CGUGGUGCGUACGAUAACGCAU
(((.[[[[[[)))...]]]]]]
>>_PKB55:_tobacco_mosaic_virus_(TMV_UPD-PK3)
AGUGUUUUUCCCUCCACUUAAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>>_PKB56:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK1)
UAACGUUGAUAGUGUUGAACUAUC
((((((.[[[[))))))...]]]]
>>_PKB57:_tobacco_mosaic_virus_(TMV_PKbulge)
UGUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAAGCGA
(((((((....[[[[((((.....((((((((.....))))))))))))))))))).......]]]]
>>_PKB58:_odontoglossum_ringspot_virus_(ORSV-S1_UPD1-PK3)
AGUGUUUGUCCCUCCACUUAAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>>_PKB59:_odontoglossum_ringspot_virus_(ORSV-S1_UPD1-PK2)
CGUGGUGCAUACGAUAAUGCAU
(((.[[[[[[)))...]]]]]]
>>_PKB60:_odontoglossum_ringspot_virus_(ORSV-S1_UPD2-PK3)
AGUGUUUAUCCCUCCACUUGAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>>_PKB61:_odontoglossum_ringspot_virus_(ORSV-S1_UPD2-PK2)
CGUUGUGUACACGAUAGUACAU
(((.[[[[[[)))...]]]]]]
>>_PKB62:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK3)
AGUGGUUAUCCCUCCACUUAAAUCGAAGGG
((((.....[[[[[))))......].]]]]
>>_PKB63:_odontoglossum_ringspot_virus_(ORSV-S1_UPD3-PK2)
CGUGGUGCAUACGAUAAUGCAU
(((.[[[[[[)))...]]]]]]
>>_PKB65:_E.coli_(Ec_16S-PK505/526)
GCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGC
((((((((...[[[[[[[......))).......]]]]]]])))))
>>_PKB66:__(TPK-70.28)
CAAGAACCGGACGGGUGAGAACCGAGACAAACACCCACCA
.......(((..[[[[[....))).......]]]]]....
>>_PKB67:_Legionella_pneumophila_(Lp_PK1)
CGAGAAGGAGAUCUCUCGUAAAUAAGACUC
(((((..[[[.[[))))).......]]]]]
>>_PKB68:_Legionella_pneumophila_(Lp_PK2)
GUUAAACCAUCACUGUGUACUGGCCAAUAAACCCAGUAUCCCGUUCGACCGAGCCCGCUUAUCGGUAU
(((.(((....((((.[[[[[[[..........)))).....))).)))............]]]]]]]
>>_PKB69:_Legionella_pneumophila_(Lp_PK3)
CGGUCAUAAGAGAUAAGCUAGCGUCCUAAUCUAUCCCGGGUUAUGGCGCGAAACUCAGGGA
(((((((((........................[[[[[[[))))))).))...]]].]]]]
>>_PKB70:_Legionella_pneumophila_(Lp_PK4)
GCUGUGUAUCAUCCUGCCCGUCGGAGGAGCCACAGUUAAAUUCAAAAGACAAGGC
((((((..((.(((.[[[.[[[))).))..))))))...........]]]..]]]
>>_PKB72:_E.coli_(Ec_S15)
GGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAA
((((.((((((.[[[[[[[))))))))))...............................]]]]]]]
>>_PKB73:_T2_bacteriophage_(T2_gene32)
CUGACCAGCUAUGAGGUCAUACAUCGUCAUAGC
.(((((.[[[[[[[))))).......]]]]]]]
>>_PKB74:_bacteriophage_T4_(T4_gene32)
UGCCAGCUAUGAGGUAAAGUGUCAUAGC
((((.[[[[[[[)))).....]]]]]]]
>>_PKB75:_hepatitis_delta_virus_("Italy"_variant)_(HDV-It_g)
UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGUCCCCUCGGUAAUGGCGAAUGGGACCCA
.(((((((..[[[[[[[{{{.[[.....}}})))))))]]....(((((((((((((...))))))))).)))).....]]]]]]]..
>>_PKB76:_hepatitis_delta_virus_("Italy"_variant)_(HDV-It_ag)
GGGUCGGCAUGGCAUCUCCACCUCCUCGCGGUCCGACCUGGGCAUCCGAAGGAGGACGCACGUCCACUCGGAUGGCUAAGGGAGAGCCA
(((((((........[[[[(((.......))))))))))...(((((((....((((....))))..)))))))......]]]].....
>>_PKB78:_AKV_murine_leukemia_virus_(AKV-MuLV)
UAGGGGGGUCAGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCACUGUCGGGGGGCA
...........((((((((.[[[[[[[)))).))))..................]]]]]]].
>>_PKB79:_gibbon_ape_leukemia_virus_(GaLV)
UAGGGGAGUCAGGGUUCGGACCCCCUCCCCGAACCUAGGGUAACACUGACUGUGGAGGGGA
...........((((((((..[[[[[[[)))))))).................]]]]]]].
>>_PKB80:_mouse_mammary_tumor_virus_(MMTV_gag/pro)
AAAAAACUUGUAAAGGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAUG
..............(((((.[[[[[[[.)))))........]]]]]]].
>>_PKB81:__(oligo_PK5)
GCGAUUUCUGACCGCUUUUUUGUCAG
(((....[[[[[)))......]]]]]
>>_PKB82:_tobacco_mosaic_virus_(TMV-L_UPD-PK1)
AUAAAGUUUGUGUUUCUAAAACACAC
..(((...[[[[)))......]]]].
>>_PKB83:_tobacco_mosaic_virus_(TMV-L_UPD-PK2)
ACGUGGUACGUACGAUAACGUACA
.(((.[[[[[[)))...]]]]]].
>>_PKB84:_tobacco_mosaic_virus_(TMV-L_UPD-PK3)
CAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
.((((.....[[[[[))))......].]]]].
>>_PKB85:_tobacco_mosaic_virus_(CcTMV_UPD-PK1)
AAGUUUGGUCGUACUUAACGACCU
.(((..[[[[[[)))..]]]]]].
>>_PKB86:_tobacco_mosaic_virus_(CcTMV_UPD-PK2)
UAGGGGCUUACCGAAAUAAGCC
.(((.[[[[[)))...]]]]].
>>_PKB87:_tobacco_mosaic_virus_(CcTMV_UPD-PK3)
CCGUGUUUAAGAGUCCACGCAAAUCGAACUCU
.((((.....[[[[[))))......].]]]].
>>_PKB88:_Feline_leukemia_virus_(FeLV)
UAGGAGAGUCAGGGCCAGGACCCCCCCCCCUGAGCCCAGGAUAACCUUAAGAAUAGGGGGGC
...........((((((((...[[[[[[)))).))))..................]]]]]].
>>_PKB89:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK1)
ACCUCGAAAGCUUAGUUUCGAGGGUCUUCUGAU
.((((((((..[[[[)))))))).....]]]].
>>_PKB90:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK2)
UGGUGGUGCACACCAAAGUGCAUA
.(((.[[[[[[)))...]]]]]].
>>_PKB91:_cucumber_green_mottle_mosaic_virus_(CGMMV_UPD-PK3)
UAGUGCUUUCCCGUUCACUUAAAUCGAACGGUU
.((((.....[[[[[))))......].]]]]..
>>_PKB92:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK1)
AAAGUCGCUGAAGACUUAAAAUUCAGG
.(((((.[[[[[)))))....]]]]].
>>_PKB93:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK2)
GGGUGGCUGAUACCAAAAUCAGCA
.(((.[[[[[[)))...]]]]]].
>>_PKB94:_tobacco_mild_green_mosaic_virus_(TMGMV_UPD-PK3)
CAGUGGUUGUUCGUCCACUUAAAUAUAACGAUU
.((((.....[[[[.))))........]]]]..
>>_PKB95:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK1)
AGUUGGACGAACAUUAAACGUCC
.(((.[[[[)))......]]]].
>>_PKB96:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK2)
CCGUGGCGAGUACGAUAACUCGUA
.(((.[[[[[[)))...]]]]]].
>>_PKB97:_pepper_mild_mottle_virus_(PMMV-S_UPD-PK3)
UAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
.((((.....[[[[[))))......].]]]].
>>_PKB98:_baboon_endogenous_virus_(BaEV)
UAGGGGUGUCAGGGCUCUGGAGCCCCCCCCGAGCCCCGGCUAACUCUAUCUGUAGGGGGGCA
...........((((((.((.[[[[[[[))))))))..................]]]]]]].
>>_PKB99:_Cas-Br-E_murine_leukemia_virus_(Cas-Br-E-MuLV)
UAGGGGGGUCGGGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGCAA
...........((((((((.[[[[[[[)))).))))..................]]]]]]]..
>>_PKB100:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK1)
AAGCCUUUUGGAUCGAAGGUUAAACGAUCCG
.((((((..[[[[[[))))))...]]]]]].
>>_PKB101:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK2)
CGCUCCUCGCUUGAGCUUGAGGCGGC
.((((.[[[[[[))))...]]]]]].
>>_PKB102:_satellite_tobacco_mosaic_virus_(STMV_UPD2-PK3)
GCGUAUCUCUUAUGUCAACAGAGA
.((((.[[[[)))).....]]]].
>>_PKB103:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK1)
CGCCGACGUGGCUGUAUAAUACGUC
.(((.[[[[)))........]]]].
>>_PKB104:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK2)
UCGUUGACAAGUACGAAAUCUUGUUA
.(((.[[[[[[.)))....]]]]]].
>>_PKB105:_satellite_tobacco_mosaic_virus_(STMV_UPD1-PK3)
UAGUGUUUUUCCCUCCACUUAAAUCGAAGGGU
.((((.....[[[[[))))......].]]]].
>>_PKB107:_simian_retrovirus-1_(SRV1_gag/pro)
GGGAAACGGACUGAGGGGCCAGCCCCAGGCCCCGAAACAAGCUUAUGGGGCG
..............((((((.[[[[[[))))))............]]]]]].
>>_PKB108:_Tetrahymena_thermophila_(T.the_telo)
UAUAACCUUCACCAAUUAGGUUCAAAUAAGUGGUA
...((((...[[[[[[[[))))....]]]]]]]].
>>_PKB109:_beet_virus_Q_(BVQ1_UPD-PKc)
UUGUGGUGCAUACAAUAAUGCAUA
.(((.[[[[[[)))...]]]]]].
>>_PKB110:_beet_virus_Q_(BVQ1_UPD-PKb)
UAGUGUUUGCCGUUCCACUUAAAUCGAAACGGA
.((((....[[[[[[))))......].]]]]].
>>_PKB111:_beet_virus_Q_(BVQ2_UPD-PKc)
ACGUGGUGCAUACGUUAAUGCAUA
.(((.[[[[[[)))...]]]]]].
>>_PKB112:_beet_virus_Q_(BVQ2_UPD-PKb)
UAGUGUUUUUCGUUCCACUUAAAUCGAAACGAU
.((((....[[[[[[))))......].]]]]].
>>_PKB113:_beet_virus_Q_(BVQ3_UPD-PKc)
UCGUGGUGCAUACGAAAAUGCAUA
.(((.[[[[[[)))...]]]]]].
>>_PKB114:_beet_virus_Q_(BVQ3_UPD-PKb)
UAGUGUUUACCGUUCCACUUAAAUCGAAACGGA
.((((....[[[[[[))))......].]]]]].
>>_PKB115:_beet_soil-borne_virus_(BSBV1_UPD-PKc)
CGGUAGCGCGAACCUUAUCGCGCA
.(((.[[[[[[)))...]]]]]].
>>_PKB116:_beet_soil-borne_virus_(BSBV1_UPD-PKb)
CAGUGUUUUGAAGUCCACUUAAAUAGAACUUCU
.((((....[[[[[[))))......].]]]]].
>>_PKB117:_beet_soil-borne_virus_(BSBV2_UPD-PKc)
ACGUGGGUUAUACGAUAAUAACCG
.(((.[[[[[[)))...]]]]]].
>>_PKB118:_beet_soil-borne_virus_(BSBV2_UPD-PKb)
CGGUGCUUUUAUGUUCACCGAAAUCGAACAUAC
.((((....[[[[[[))))......].]]]]].
>>_PKB119:_beet_soil-borne_virus_(BSBV3_UPD-PKc)
ACGUGGCGAAUACGAUAAUUCGUA
.(((.[[[[[[)))...]]]]]].
>>_PKB120:_beet_soil-borne_virus_(BSBV3_UPD-PKb)
UAGUGUUCGUGGAUAACACUUUAAUUAAGAUUCAUA
.((((((.[[[[[[)))))).........]]]]]].
>>_PKB121:_satellite_tobacco_necrosis_virus_1_(STNV1_PK1)
AAGCAGUCCCAGCUCUGCAUUGGGAA
.(((..[[[[[)))......]]]]].
>>_PKB122:_satellite_tobacco_necrosis_virus_1_(STNV1_PK2)
UACUACUUGCUCAUUUGUAGUCUAAAUGAGA
.(((((...[[[[[[[)))))..]]]]]]].
>>_PKB123:_satellite_tobacco_necrosis_virus_1_(STNV1_PK3)
GACGUUGGCCUCGACGUGUCGAGGUG
.((((..[[[[[[))))..]]]]]].
>>_PKB124:_satellite_tobacco_necrosis_virus_2_(STNV2_PK1)
CAGUAGUCCUGAACUAGUAAAUCAGGACC
.(((.[[[[[[[)))......]]]]]]].
>>_PKB125:_satellite_tobacco_necrosis_virus_2_(STNV2_PK2)
CCAUUCCCACUAGUGUAUUAGUGGA
.(((..[[[[[[)))...]]]]]].
>>_PKB126:_satellite_tobacco_necrosis_virus_2_(STNV2_PK3)
GAACGAGGCCCCGCGUGAAUUGGGGUG
..(((..[[[[[[)))....]]]]]].
>>_PKB130:_tobacco_rattle_virus_(TRV-PSG)
AGGGGUAAAACCCCUCGCCUACGUAAGCGUUAUUACGCCC
...............(((...[[[[[)))...]]]]]...
>>_PKB131:__(NGF-H1)
CGCUCAACUCAUGGAGCGCAAGACGAAUAGCUACAUAUUCGACAUGAG
(((((..[[[[[[))))).....((((((......)))))).]]]]]]
>>_PKB132:__(NGF-L2)
CGCUCAACCUCAGAGCGCAAGAGUCGAACGAAUACAGUUCGACAUGAGG
(((((..[[[[[))))).....(((((((.......))))))).]]]]]
>>_PKB133:__(NGF-L6)
CGCUCAACUCAUGGAGCGCACGACGGAUCACCAUCGAUUCGACAUGAG
(((((..[[[[[[))))).....((((((......)))))).]]]]]]
>>_PKB138:_barley_stripe_mosaic_virus_(BSMVbeta)
AUUGGUAUGUAAGCUACAACUUCCGGUAGCUGCGUCACACUUUAAGAGUGUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCCCCAAGGGAAGACCA
.((((((((..((((((..[[[[[.))))))....((((((.....)))))))))))))).((((((.....)))))).........]]]]]....
>>_PKB139:_tobacco_mosaic_virus_(TMV-L_PKbulge)
UAGUGUCUUGGAGCGCGCGGAGUAAACAUAUAUGGUUCAUAUAUGUCCGUAGGCACGUAAAAAAAGCGAG
..((((((....[[[[((((.....((((((((.....)))))))))))))))))).........]]]].
>>_PKB140:_cucumber_green_mottle_mosaic_virus_(CGMMV_PKbulge)
UUUGCUCAUUGGUUUGCGGAAACCUCUCACGUGUGACGUUGAAGUUUCUAUGGGCAGUAAUUCUGCAAG
.((((((((....[[[[((((((.((..(((.....))).)).)))))))))))))).......]]]].
>>_PKB141:_tobacco_mild_green_mosaic_virus_(TMGMV_PKbulge)
UUGUCAUAUCUGGAUCCAACAGUUAAACCAUGUGAUGGUGUAUACUGUGGUAUGGCGUAAAACAUCGGAG
.(((((((((....[[[.(((((...((((.....))))....)))))))))))))).........]]].
>>_PKB142:_satellite_tobacco_mosaic_virus_(STMV_PKbulge)
UUUUGUUUUGGUCUUCCCGAACGCAUACGUUAGUGUGACUACCGUUGUUCGAAACAAGUAAAACAGGAAGG
.(((((((....[[[[[((((((...(((.(((.....))).)))))))))))))))).......]]]]].
>>_PKB143:_pepper_mild_mottle_virus_(PMMV-S_PKbulge)
UUGUCGUUGGGAUGGAACGCAAUUAAAUACAUGUGUGACGUGUAUUUGCGAACGACGUAAUUAUUUUUCAG
.(((((((....[[[[[(((....(((((((((.....)))))))))))))))))))........]]]]].
>>_PKB144:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge1)
UUGUGUAUAUGGAUCAUGCGGAUAAAGUUAUACUGGUGCAGUAUAACCCGUUAUACACAUAAAAUUAUGAG
.((((((((....[[[[((((.....((((((((.....)))))))))))))))))))).......]]]].
>>_PKB145:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge2)
UUGUGUCAGACGCGUGUAAGGAGUGGUCAACCUUACGACACAUUUAAAUAAUGCGUCC
.(((((..[[[[[[(((((((.........)))))))))))).........]]]]]].
>>_PKB146:_odontoglossum_ringspot_virus_(ORSV-S1_PKbulge3)
UUUCACUGCGGAUAUGUAGGUUUCCUCGGUGAAUAUAAAACUUAUAUCCC
.(((((...[[[[[((.(((...))))))))))...........]]]]].
>>_PKB147:_Saccharomyces_cerevisiae_(Sc_18S-PKE21-7/8)
AUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGU
.((((((((((...[[..[[[[[[)))))))))).......]]]]]].]].
>>_PKB151:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK1)
AAAUGUUUGAUCAGAUCAUUCAAAUCUGAUGG
.((((....[[[[[[[))))...]]]]]]]..
>>_PKB152:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK2)
UGGUGCCCAUCAACCAUAUGAUGGGA
.(((.[[[[[[[)))...]]]]]]].
>>_PKB153:_barley_stripe_mosaic_virus_(BSMVbeta_UPD-PK3)
GAGUGUUUGCAAGUCCACUAUAAUCGAACUUGA
.((((....[[[[[[))))......].]]]]].
>>_PKB154:_brome_mosaic_virus_(BMV3_UPD-PK1)
GAGCCCCUGACUGGGUUAAAGUCACA
.(((((.[[[[[)))))..]]]]]..
>>_PKB155:_brome_mosaic_virus_(BMV3_UPD-PK2)
CCCUUGUCUCAGGUAGAGACC
.(((.[[[[[)))..]]]]].
>>_PKB156:_brome_mosaic_virus_(BMV3_UPD-PK3)
ACUUUGGCUAAGGUUAAAAGCUU
.(((.[[[[)))......]]]].
>>_PKB157:_brome_mosaic_virus_(BMV3_UPD-PK4)
UUGUUGAAUCAGUACAAUAACUGAUA
.(((...[[[[[[)))...]]]]]].
>>_PKB158:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK1)
CUUUAAGGGACCUUGUGAAAUUCAAGGG
.((((.....[[[[[))))...]]]]].
>>_PKB159:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK2)
GGGCGGGUGUCGCCAGAAAUCACCG
.(((.[[[[[.)))....].]]]].
>>_PKB160:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK3)
CGAUACUACUAGUUGUAUCAAAACAAAACUAA
.(((((...[[[[[))))).......]]]]].
>>_PKB161:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK4)
AGGUGGAUGUUACCAUAAACAUUA
.(((.[[[[[[)))...]]]]]].
>>_PKB162:_tobacco_rattle_virus,_strain_PSG_(TRV-PSG2_PK5)
UAAUGUCGCAGGUGGCAUUUUAAAAUAAGACCUGA
.((((((.[[[[[))))))..........]]]]].
>>_PKB163:_Homo_sapiens_(Hs_SRP-pkn)
GCCGGGCGCGGUGGCGCGUGCCUGUAGUCCCAGCUACUCGGGAGGCU
(((.((((((.[[[[.)))))).....((((.]]]]...))))))).
>>_PKB164:_poa_semilatent_virus_(PSLVbeta)
AUUGGUAUGUAAGCUACUUCUUCCAGUAGCUGCGUCAUAACAUCAAGGUUAUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCUCCAAGGAAGACCA
.((((((((..((((((..[[[[[.))))))....((((((......)))))))))))))).((((((.....))))))........]]]]]....
>>_PKB165:_poa_semilatent_virus_(PSLVbeta_UPD-PK1)
AUUGCCACUGUGGAAAUCAGUGA
.(((.[[[[[)))....]]]]].
>>_PKB166:_poa_semilatent_virus_(PSLVbeta_UPD-PK2)
CGGUUUUAUCUACCAUAAGAUAAA
.(((.[[[[[[)))...]]]]]].
>>_PKB167:_poa_semilatent_virus_(PSLVbeta_UPD-PK3)
AAGUGUUUUCAUGUCCACUUAAAUCGAACAUGAAC
.((((..[[[[[[[[))))......].]]]]]]].
>>_PKB169:_Coxsackie_B_virus_(CoxB3)
ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAAAAAA
.((((((((((((.[[[[[[.........)))))))))))).....((.(((((.]]]]]]))))).))....
>>_PKB172:_bamboo_mosaic_virus_(BaMV)
CUUUUGGUUUCUACAGUUUUUUCCAAAAAAAAAAAAAAA
.((((((.........[[[[[[))))))...]]]]]]..
>>_PKB173:_Satellite_cereal_yellow_dwarf_virus-RPV_RNA_(satRPV)
ACAGAGCGCGUACUGUCUGACGACGUAUCCGCGCGGACUAGAAGGCUGGUGCCUCGUCCAACAAAUAGAUACA
((((.[[[[[..))))........(((((]]]]]((((....((((....)))).))))........))))).
>>_PKB175:__(biotin-PK)
CACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGC
.(((((.[[[[[[[)))))..............................]]]]]]].
>>_PKB176:__(biotin-PK-AN69.1)
GGACCGUCAGAGGACACGGUUAAAAAGUCCUCU
..(((((..[[[[[[)))))......]]]]]].
>>_PKB177:_Rattus_rattus_(black_rat)_(Rr_ODCanti)
UGCUCCUGAUGUCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAACAGUCAGCGGGAUCACAGU
............(((((.((((((......[[[[[[.)))))).)))))..........]]]]]].....
>>_PKB182:_soil-borne_rye_mosaic_virus_(SBRMV1-PKa)
GGGGUUCAAAUCCCCCCCCGAACCGGAGGGUUAUCCGGCCCA
...............(((....[[[[[)))...]]]]]....
>>_PKB183:_soil-borne_rye_mosaic_virus_(SBRMV1-UPD-PKb)
ACGUCGUGCAGUACGGUAAACUGCACA
.(((.[[[[[[[)))....]]]]]]].
>>_PKB184:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKc)
UUCUGUUUUUCGAACAGAUGUAAAUCGAAGA
.(((((.[[[[[[)))))......]]]]]].
>>_PKB185:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKd)
ACGUGGCCAUCACGAUAGAUGGUU
.(((.[[[[[[)))...]]]]]].
>>_PKB186:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKe)
AAGCCUAUUUGUACGGGUUGAGUACAAAC
.(((((.[[[[[..)))))....]]]]].
>>_PKB187:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKf)
GCCGCUGGGAUUGCGGAUUAUAAAUCG
.((((...[[[[))))......]]]].
>>_PKB188:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKg)
UCGUUGCCGUCACGAUAGACGGA
.(((..[[[[[)))...]]]]].
>>_PKB189:_soil-borne_rye_mosaic_virus_(SBRMV1_UPD-PKh)
AGUCUAACAUGUCGGGCUGAGACAUGUC
.((((.[[[[[[[))))...]]]]]]].
>>_PKB190:_Plautia_stali_intestine_virus_(PSIV_IRES)
CUCGCUCAAACAUUAAGUGGUGUUGUGCGAAAAGAAUCUCACUUCAA
.((((...(((((.[[[[[)))))..)))).........]]]]]...
>>_PKB194:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKb)
UACGCUGUACAGUGCGUUAAACUGUACA
..(((.[[[[[[[)))....]]]]]]].
>>_PKB195:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKc)
CUCUGUUGAUCAAACAGAAAUAAAUUGAUUA
.(((((.[[[[[[)))))......]]]]]].
>>_PKB196:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKd)
ACGCGGUCAUUGCGAUAAAUGACU
.(((.[[[[[[)))...]]]]]].
>>_PKB197:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKe)
GAACCUAUUUGCUCGGGUUGAGUGCAAAC
..((((.[[[[[..)))).....]]]]].
>>_PKB198:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKf)
ACCGCCUGAUUAGCGGUCUACAAGUUAAUCGA
.((((..[[[[[)))).........]]]]]..
>>_PKB199:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKg)
UCGUGGUCAGUACGAUAACUGAU
.(((..[[[[[)))...]]]]].
>>_PKB200:_soil-borne_wheat_mosaic_virus_(SBWMV1_UPD-PKh)
AGUCUAAUUUGUCGGGCUGAGACAAAUC
.((((.[[[[[[[))))...]]]]]]].
>>_PKB201:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKb)
GGCGUUCUACAGUACGUUUAAACUGUAGG
..(((.[[[[[[[))).....]]]]]]].
>>_PKB202:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKi)
UGGUGCUUGUUAUUUCACCUAAAUCGAAAUAACG
.((((...[[[[[[[)))).......]]]]]]].
>>_PKB203:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKk)
ACGUGGUCUUCACGAUAGAAGAUG
.(((.[[[[[[)))...]]]]]].
>>_PKB204:_soil-borne_wheat_mosaic_virus_(SBWMV2_UPD-PKl)
CAGAGUUAUCAUACUCUAUAAACUAUGAC
.((((...[[[[[))))......]]]]].
>>_PKB205:_Palmaria_palmata_(Pp_18S-PKE23-9/12)
UUAGAGUGUUCAAAGCCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAA
.((..((.[[[[..))(((((....))).))..))........]]]].
>>_PKB206:_Homo_sapiens_(Hs_PrP)
GCCUCAUGGUGGUGGCUGGGGGCAGCCUCAUGGUGGUGGCUGGGG
...((((((.............[[[[[))))))....]]]]]...
>>_PKB207:_Bos_Taurus_(cow)_(Bt_PrP)
GCCCCAUGGAGGUGGCUGGGGCCAGCCUCAUGGAGGUGGCUGGGG
...((((((............[[[[[[))))))....]]]]]]..
>>_PKB210:_Bordetella_pertussis_(Bp_PK2)
CCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGGGGAAGGCAACUUCCCAGGGGGCAACCCCGAACCGCAGCAGCGACAUUCACAAGGAAU
.((((((..(((...[[[[[[[..))).((((((((((....)))))).((((....))))...)))).)))))).......]]]]]]].
>>_PKB212:_Plautia_stali_intestine_virus_(PSIV_IRES-PKIII)
AGGUCUUGUAUAUUUAUACUUACCACACAAGAUGGACCGGAGCAGCCCUCCAAUAUCUAGUGUA
.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
>>_PKB213:_Himetobi_P_virus_(HiPV_IRES-PKI)
CAGCCUUGUAGUUUUAGUGGACUUUAGGCUAAAGAAUUUCACUAG
.(((((...((((.[[[[[))))..))))).........]]]]].
>>_PKB215:_Himetobi_P_virus_(HiPV_IRES-PKIII)
GACCCUUAGUUAUUUAGCUUUACCGCCCAGGAUGGGGUGCAGCGUUCCUGCAAUAUCCAGGGCA
.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
>>_PKB216:_Drosophila_C_virus_(DCV_IRES-PKI)
CUUCUUAUAUGAUUAGGUUGUCAUUUAGAAUAAGAAAAUAACCUG
.((((...(((((.[[[[[)))))..)))).........]]]]].
>>_PKB218:_Porcine_reproductive_and_respiratory_syndrome_virus,_North_American_isolate_(16244B)_(PRRSV-16244B)
UUUAAACUGCUAGCCGCCAGCGGCUUGACCCGCUGUGGUCGCGGCGGCUUGGUUGUUACUGAGACAGCGGUA
............((((((.((((((....[[[[[[[))))))))))))...............]]]]]]]..
>>_PKB220:_Drosophila_C_virus_(DCV_IRES-PKIII)
UUAGGUUAACUAUUUAGUUUUACUGUUCAGGAUGCCUAUUGGCAGCCCCAUAAUAUCCAGGACA
.((((..((((....)))).....[[[[.[[[[[)))).(((.....)))...]]]]].]]]].
>>_PKB221:_Cricket_paralysis_virus_(CrPV_IRES-PKI)
CGGUUUUUCAGAUUAGGUAGUCGAAAAACCUAAGAAAUUUACCUG
.((((((...(((.[[[[[)))..)))))).........]]]]].
>>_PKB223:_Cricket_paralysis_virus_(CrPV_IRES-PKIII)
UUAGGUUAGCUAUUUAGCUUUACGUUCCAGGAUGCCUAGUGGCAGCCCCACAAUAUCCAGGAAG
.((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]].
>>_PKB224:_Triatoma_virus_(TrV_IRES-PKI)
UUUCCUAUACCUCGAGUCGGGUUUGGAAUCUAAGGUUGACUCG
.((((...((((.[[[[[))))..)))).........]]]]].
>>_PKB226:_Triatoma_virus_(TrV_IRES-PKIII)
UGCGCUUGCCUAUUUAGGCAUACUUCUCAGGAUGGCGCGUUGCAGUCCAACAAGAUCCAGGGAC
.((((..((((....)))).....[[[[.[[[[.))))((((.....))))...]]]].]]]].
>>_PKB227:_Black_queen_cell_virus_(BQCV_IRES-PKI)
AUGUUUAGAAGAUUAGGUAGUCUCUAAACAGAACAAUUUACCUG
.(((((...((((.[[[[[))))..)))))........]]]]].
>>_PKB229:_Black_queen_cell_virus_(BQCV_IRES-PKIII)
AUCACCGUACCUAUUUAGGUUUACGCUCCAAGAUCGGUGGAUAGCAGCCCUAUCAAUAUCUAGGAGA
..((((..((((....)))).....[[[[.[[[[.))))(((((.....)))))...]]]].]]]].
>>_PKB230:_Rhopalosiphum_padi_virus_(RhPV_IRES-PKI)
CAGGAGAGCAUACGCUAGGUCGCGUUGACUAUCCUUAUAUAUGACCUG
.((((.((((.((((.[[[[[)))))).)).)))).......]]]]].
>>_PKB232:_Rhopalosiphum_padi_virus_(RhPV_IRES-PKIII)
UUGGUUAGCUAUUUAGCUUUACUAAUCAAGACGCCGUCGUGCAGCCCACAAAAGUCUAGAUA
.(((..((((....))))......[[[.[[[[.)))..(((.....)))....]]]].]]].
>>_PKB233:_Porcine_reproductive_and_respiratory_syndrome_virus,_European_Lelystad_strain_(LV)_(PRRSV-LV)
UUUAAACUGUUAGCCGCCAGCGGCUUGACCCGCUGUGGCCGCGGCGGCCUAGUUGUGACUGAAACGGCGGU
............((((((.((((((....[[[[[[[))))))))))))...............]]]]]]].
>>_PKB234:_Variovorax_paradoxus_(Vp_PK2)
GCCUUGCAACAGUUGGCCGAUGGGCUGGGCAAGGGGGUCUGGAGCAAUCCUGACCUCCCGGCUGCAAGGAUAACUACAUGGGCU
.((((((..(((...[[[[[[[..))).(((((((((((((((....))))))))))))))).)))))).......]]]]]]].
>>_PKB235:_Giardiavirus_(GLV_IRES)
GGAGACCCAUGGAGAGUCUCCAGAGGUUCCUAAGGCCUCGAUCGCGCCUGCCGGGAGGCAGAAUGUCCCGGUUCUCC
((((((....[[[[[)))))).(((((.......)))))..........(((((((.........)))))))]]]]]
>>_PKB237:_West_Nile_virus_(WNV_PK3end)
ACCUGGGAUAGACUAGGGGAUCUUCUGCUCUGCACAACCAGCCACACGGCACAGUGCGCCGACAUAGGUGGCUGGUGGUGCUAGAACACAGGAUCU
.(((((..[[[[)))))......]]]].(((((((.(((((((((.((((.......))))......))))))))).)))).)))...........
>>_PKB238:_Dengue_virus_type_2_(DEN2_PK1)
AUGGGGGCCCAAGGUGAGAUGAAGCUGUAGUCUCACUGGAAGGACUAGAGGUUAGAGGAGACCCCCCCAAAACAAAAAACAGCA
.((((((((...((((((((...[[[[[.))))))))....))......((((......)))))))))).........]]]]].
>>_PKB240:_beet_chlorosis_virus_(BChV)
GGGAAAUGGACUGAGCGGCGCCGACCGCCAAACAACCGGCA
..............((((.[[[[.))))........]]]].
>>_PKB241:_Montana_Myotis_leukoencephalitis_virus_(MMLV_PKb)
AGAGAGUUAUUCGCUCCUCUCGAGAUUGAGCGGC
.(((((....[[[[[[)))))......]]]]]].
>>_PKB242:_Rio_Bravo_virus_(RBV_PKb)
UGAGGUUUUUCCCCUCCCUCAUGAUGAGGGGAAG
.((((...[[[[[[[[)))).....]]]]]]]].
>>_PKB244:_hepatitis_A_virus_(HAV)
UUAAACAAAUUUUCUUAAAAUUUCUGAGGUUUGUUUAUUUCUUUUAUCAGUAAAU
.((((((((((.........[[[[[[[)))))))))).........]]]].]]].
>>_PKB245:_Human_Parechovirus_1_(HPeV1)
CCCAGCCUUGGGGUGGCUGGUCAAUAAAAACCCCC
.((((((..[[[[[)))))).........]]]]].
>>_PKB247:_Nemesia_ring_necrosis_virus_(NeRNV_PKa)
CCCCUGUCCCGGGUAGGGAACC
.(((..[[[[)))..]]]]...
>>_PKB248:_Nemesia_ring_necrosis_virus_(NeRNV_PKb)
UGUUCCUUGGAUUGCUACGUUCACCAGAUUUGUGUAAUCUGGCCGUUAGGAACUUAAAAUUGCGCG
.((((((.....[[[((((....(((((((.....))))))).))))))))))........]]]..
>>_PKB249:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK1)
UAGUGUUUCGGCUUCCACUUAAAUCGAAAGCCA
.((((....[[[[[[))))......].]]]]].
>>_PKB250:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK2)
GGGUGGCGCACACCACAGUGCGUA
.(((.[[[[[[)))...]]]]]].
>>_PKB251:_Nemesia_ring_necrosis_virus_(NeRNV_UPD-PK3)
CAGCCUCUCACAGCUUCCUCGUGAGG
.(((..[[[[[.))).....]]]]].
>>_PKB253:_White_Bream_Virus_(WBV)
UUUAAACUGGUGGGGCAGUGUCUAGGAUUGACGUUAGACACUGCUUUUUGCCCGUUUCAAACAGGUGAAUACAAACCGUCAU
...........((((((((((((((...[[[[[)))))))))))))).............................]]]]].
>>_PKB254:_SARS_coronavirus_(SARS-CoV)
UUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUCUACAGGGCUU
............(((((((((((...[[[[[[[)))))))))))((((((((.........))).)))))...]].]]]]].
>>_PKB255:_mouse_hepatitis_virus_(MHV)
CUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGA
.((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]].
>>_PKB256:_bovine_coronavirus_(BCV)
CUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGA
.((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]].
>>_PKB257:_Mus_musculus_(mouse)_(Mm_Edr)
GGGAAACUCCCCGGCCCCGCUGUAGGGGGACCUUCAGCGACAGGGCCAGAACGAAUAAGGUCCCCA
............((((((((((...[[[[[[[[[)))))...))))).........]]]]]]]]].
>>_PKB258:_Homo_sapiens_(Hs_Ma3)
GGGAAACGGGAACUGGGCUUGGGACAAGAGCCAUCCCAAGUCCAAGGCCAAGUAGGCUCG
.............(((((((((((...[[[[[.)))))))))))..........]]]]].
>>_PKB259:_potato_yellow_vein_virus_(PYVV1)
CGGUAGAAAAGAUGGUUUAAACCACGCCUUCUACCAAGUUAGUAAAUAAAUAGGCGG
.((((((.....((((....))))[[[[[))))))................]]]]].
>>_PKB260:_potato_yellow_vein_virus_(PYVV2)
AGUAGAAAAGUUGGUGCUUAGACCACGCCCUCUACCGUAAUAAUAGAUAAAUAGGCG
.(((((.....((((......))))[[[[.)))))..................]]]]
>>_PKB261:_potato_yellow_vein_virus_(PYVV3)
CGGUAGAAAAGAUGGUUUGAAAACCACGCCUUCUACCAAUAUAGUAAAUAAAUAGGCGG
.((((((.....(((((....)))))[[[[[))))))................]]]]].
>>_PKB262:_cucumber_yellows_virus_(CuYV1)
CGUUUGGUCGAAUGCUACUAGAGCAGCCUGACCAAACUAGUAUUAGUAAAUAAAGG
.((((((((...((((.....)))).[[[))))))))................]]]
>>_PKB263:_cucurbit_yellow_stunting_disorder_virus_(CYSDV1)
CGACACUCUAAAGAGUUCCGUGAGGAACCACCUUGAGUGUCUAGUUAUAAAUAAACUAGGUC
.(((((((......(((((....))))).[[[[.)))))))................]]]].
>>_PKB264:_cucurbit_yellow_stunting_disorder_virus_(CYSDV2)
CGACACUCUAAAGUGUUCCAAGAGGAACCACCUUGAGUGUCUAGUUAUAAAUAAACUAGGUC
.(((((((......(((((....))))).[[[[.)))))))................]]]].
>>_PKB265:_sweet_potato_chlorotic_stunt_virus_(SPCSV1)
CGGUUUUCCUAAAUCGUCGUGAGACGGACCUUGGAAAACCUAGUAUUUAAAUAACUAGGUC
.((((((((.....((((....))))[[[[[.))))))))................]]]]]
>>_PKB266:_lettuce_infectious_yellows_virus_(LIYV1)
UGUCUUCCUAAAAUCCUUGGAAGACUGUAUAUAUAGAAUAAAGGUCG
.(((((((......[[[[)))))))...............]]]]...
>>_PKB267:_little_cherry_virus_1_(LChV-1)
AAUGCAACUUUUAAAUAGUUUAUCUGUUAAGAUAAACCACCUAGGUUGCAUAUAUAAAAAAUAAAAGGUGCC
.(((((((((.......((((((((....))))))))[[[[[)))))))))..............]]]]]..
>>_PKB268:_beet_yellows_virus_(BYV)
CUCCUAGCGAAGUCCCGCUAGGAAGAAAAAAUAAGGGCCG
.(((((((...[[[[.)))))))...........]]]]..
>>_PKB269:_citrus_tristeza_virus_(CTV)
AGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACGCACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
.(((((((.......((((((((......))))))))....[[[[[)))))))....]]]]]....
>>_PKB270:_Pineapple_mealybug_wilt_associated_virus_-_2_(PMWaV-2)
CAAAGUCCUAUAAACCUCAAUAAUCCCUCGUUAGGAGGGACACGCGAGGACUUUGGCGUGCC
.((((((((..............((((((.....))))))[[[[[.)))))))).]]]]]..
>>_PKB271:_Grapevine_leafroll-associated_virus_-_2_(GLRaV-3)
ACGCCAAAAUCCAAUUAAAGUUUGGGACCUAGGCGGGCCUCUUACGAGGCUAACUUAUCGACAAUAAGUUAGGUC
.((((.....((((.......))))[[[[[[))))((((((....))))))..................]]]]]]
>>_PKB272:_strawberry_chlorotic_fleck_associated_virus_(SCFaV)
ACUGUGAUUAUAAAAGUGGAGUACUAAAGUACCCACUACCUUUAAUCACAGACAAUAAAGGUCCAU
.((((((((.....(((((.((((....)))))))))[[[[[[)))))))).....]]]]]]....
>>_PKB273:_influenza_A_virus,_strain_A/PR/8/34_(IAV_PK_NS)
UUCCAGGACAUACUGCUGAGGAUGUCAAAAAUGCAGUUGGAGUCCUCA
.(((((...........[[[[[[.............)))))]]]]]].
>>_PKB274:_influenza_B_virus,_strain_B/Victoria/02/1987_(IBV_PK_NS)
ACUGAUGAUCUUACAGUGGAGGAUGAAGAAGAUGGCCAUCGGAUCCUCA
.((((((...........[[[[[[............))))))]]]]]].
>>_PKB275:_Bacillus_subtilis_(Bs_glmS_P3.1)
CCGGCUGAGUGUGCAGAUCACAGCCGUAAGAAUUUCUUCAAACCAAGGGGGUGACUCCUUGAACAAAGAGAAAUCACAUGAUCUU
.((((((.......[[[[[[)))))).....(((((((.....(((((((....)))))))......)))))))....]]]]]].
>>_PKB276:_Bacillus_subtilis_(Bs_glmS_P1.1)
CGCCCGAACUAAGCGCCCGGAAAAAGGCUUAGUUGACGAGGAUGGAGGUUAUCGAAUUUCGCGGAUCCUCCCG
.(((((((((((((............)))))))).........[[[[[....(((...))))))))]]]]]..
>>_PKB277:_tobacco_etch_virus_(TEV_PK1)
CGAAUCUCAAGCAAUCAAGCAUUCUACUUCUAUUGCA
.((((((...[[[[[..)).)))).......]]]]].
>>_PKB278:_tobacco_etch_virus_(TEV_PK2)
AUUUAAAUCAUUUCUUUUAAAGCAAAAGC
.((((((...[[[..))))))....]]].
>>_PKB279:_tobacco_etch_virus_(TEV_PK3)
CAAUUUUCUGAAAAUUUUCAC
.(((((..[[[))))).]]].
>>_PKB280:_Visna-Maedi_virus_(VMV)
GGGAAACAACAGGAGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGUUGUAACAGAAGCACCACC
.............(((((((.....[[[[[[[.......)))))))..............]]]]]]].
>>_PKB281:_sugarcane_yellow_leaf_virus_(ScYLV)
GGGAAACGAGCCAAGUGGCGCCGACCACUUAAAAACACCGGAA
.............(((((..[[[.))))).........]]]..
>>_PKB282:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKI)
CCGUCGUUUCCGACGUAAAAGGAAGCAA
.((((..[[[[)))).....]]]]....
>>_PKB283:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKII)
CCGCCUGUCCCGGCGUUAAAGGGAAGUAA
.((((..[[[[)))).....]]]].....
>>_PKB284:_foot-and-mouth_disease_virus,_serotype_A_(FMDV-A_PKIII)
ACCGCCUACCCCGGCGUUAACGGGGAACAA
..((((..[[[[)))).....]]]].....
>>_PKB285:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKI)
ACCGUCGUUCCCGACGUAAAAGGGAGG
..((((..[[[[)))).....]]]]..
>>_PKB286:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKII)
ACCGUCCGGCCCGACGUAAAAGGGUGGUAA
..((((...[[[)))).....]]]......
>>_PKB287:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKIII)
CCGUCUUUCCCGACGUUAAAGGGAUG
.((((..[[[[)))).....]]]]..
>>_PKB288:_foot-and-mouth_disease_virus,_serotype_O_(FMDV-O1K_PKIV)
CCUUCGCUCGGAAGUAAAACGACAA
.((((..[[[)))).....]]]...
>>_PKB289:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKI)
ACCGUCGUUCCCGACGUAAAAGGGAUGU
..((((..[[[[)))).....]]]]...
>>_PKB290:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKII)
ACCGUCUCUCCCGACGUUAAAGGGAUGUAA
..((((..[[[[)))).....]]]].....
>>_PKB291:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKIII)
CCGCCUAUCCCGGCGUUAAUGGGAGG
.((((..[[[[)))).....]]]]..
>>_PKB292:_foot-and-mouth_disease_virus,_serotype_C_(FMDV-C_PKIV)
CCUUCACCUGGAAGUAAAACAGCAA
.((((..[[[)))).....]]]...
>>_PKB293:_encephalomyocarditis_virus_(EMCV-R_PKB)
ACGUGAAGGCUACGAUAGUGCCAG
.((((..[[[)))).....]]]..
>>_PKB294:_encephalomyocarditis_virus_(EMCV-R_PKC)
AGGGCGGGUACUGCCGUAAGUGCCA
..(((.[[[[[[)))...]]]]]].
>>_PKB295:_Mengovirus_(Mengo_PKB)
ACGUGAAGGCUACGAUAGUGCCAG
.((((..[[[)))).....]]]..
>>_PKB296:_Mengovirus_(Mengo_PKC)
AGGGCGGGUCCUGCCGAAAGUGCCAA
..(((.[[[.[[)))...]].]]]..
>>_PKB297:_hepatitis_A_virus_(HAV_PK1)
AAGUCCAUGGUGAGGGGACUUGAUACCUCACCG
.(((((..[[[[[[[))))).....]]]]]]].
>>_PKB298:_hepatitis_A_virus_(HAV_PK2)
CGCCGUUUGCCUAGGCUAUAGGCUAAAUU
.(((....[[[[[)))..]]]]]......
>>_PKB299:_Theiler's_murine_encephalomyelitis_virus_(TMEV)
ACGCGGGUACUGCGAUAGUGCCACC
.(((.[[[[[[)))..]]]]]]...
>>_PKB300:__(antiHIV1-RT_1.1)
UCAAGAAUUCCGUUUUCAGUCGGGAAAAACUGAACAA
.......(((((..[[[[[[)))))...]]]]]]...
>>_PKB301:__(antiHIV1-RT_1.3a)
GAAUAUCUUCCGAAGCCGAACGGGAAAACCGGCAUCU
.......(((((..[[[[..)))))....]]]]....
>>_PKB302:__(antiHIV1-NC_psi-50-1)
GCCAGUGGUUUGCAAUGCUGGUCCGGUGCGU
(((((((...[[[[.)))))))....]]]].
>>_PKB303:_Bombyx_mori_(R2_retroPK)
AGCCCCGAUGGACGGACCGCGAGGACCGUCAAGCCUAGCAGGUACCUUCGGGUGGGGCCUUGCGAUACCUGCGGGC
.(((((....(((((.((....)).)))))...[[[.[[[[[[(((....))))))))........]]]]]]]]].
>>_PKB304:_B._subtilis_(SBU)
AGAGGUUCUAGCUACACCCUCUAUAAAAAACUAA
(((((...[[[......)))))........]]].
......@@ -360,8 +360,8 @@ def launch_RNAMoIP(seq_, header_, basename):
ninsertions = [ t[1] for t in results if t[0] != ""]
scores = [ t[2] for t in results if t[0] != ""]
rna = open(outputDir + basename + ".moip", "w")
rna.write(header_)
rna.write(seq_)
rna.write(header_+'\n')
rna.write(seq_+'\n')
for p,n,s in zip(predictions, ninsertions, scores):
rna.write(p+'\t'+str(n)+'\t'+str(s)+'\n')
rna.close()
......@@ -885,8 +885,8 @@ class RNA:
if ss not in self.biorseoBGSUBayesPairA.predictions:
self.biorseoBGSUBayesPairA.predictions.append(ss)
self.biorseoBGSUBayesPairA.ninsertions.append(lines[i].count('+'))
else:
print(targetdir+ self.basename + ".bgsubypA not found !")
# else:
# print(targetdir+ self.basename + ".bgsubypA not found !")
def get_biorseoBGSUBayesPairB_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bgsubypB"):
......@@ -898,8 +898,8 @@ class RNA:
if ss not in self.biorseoBGSUBayesPairB.predictions:
self.biorseoBGSUBayesPairB.predictions.append(ss)
self.biorseoBGSUBayesPairB.ninsertions.append(lines[i].count('+'))
else:
print(targetdir+ self.basename + ".bgsubypB not found !")
# else:
# print(targetdir+ self.basename + ".bgsubypB not found !")
def get_biorseoBGSUBayesPairC_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bgsubypC"):
......@@ -911,8 +911,8 @@ class RNA:
if ss not in self.biorseoBGSUBayesPairC.predictions:
self.biorseoBGSUBayesPairC.predictions.append(ss)
self.biorseoBGSUBayesPairC.ninsertions.append(lines[i].count('+'))
else:
print(targetdir+ self.basename + ".bgsubypC not found !")
# else:
# print(targetdir+ self.basename + ".bgsubypC not found !")
def get_biorseoBGSUBayesPairD_results(self, targetdir):
if path.isfile(targetdir+ self.basename + ".bgsubypD"):
......@@ -924,8 +924,8 @@ class RNA:
if ss not in self.biorseoBGSUBayesPairD.predictions:
self.biorseoBGSUBayesPairD.predictions.append(ss)
self.biorseoBGSUBayesPairD.ninsertions.append(lines[i].count('+'))
else:
print(targetdir+ self.basename + ".bgsubypD not found !")
# else:
# print(targetdir+ self.basename + ".bgsubypD not found !")
def load_results_from(self, targetDir):
self.get_biokop_results()
......@@ -1003,9 +1003,9 @@ for nt, number in ignored_nt_dict.items():
tot = len(RNAcontainer)
print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudoknots." % (tot, pk_counter))
# # ================= PREDICTION OF STRUCTURES ===============================
# #================= PREDICTION OF STRUCTURES ===============================
# # define job list
# #define job list
# joblist = []
# for instance in RNAcontainer:
# basename = instance.basename
......@@ -1017,7 +1017,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
# # BayesPairing and BGSUBayesPairing
# joblist.append(Job(function=launch_BayesPairing, args=["rna3dmotif", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BayesPairing, checkArgs=[basename]))
# joblist.append(Job(function=launch_BayesPairing, args=["3dmotifatlas", instance.seq_, instance.header_, basename], how_many_in_parallel=-1, priority=3, checkFunc=check_BGSUBayesPairing, checkArgs=[basename]))
# # bmotinBGSUJAR3DA-D
# # biorseoBGSUJAR3DA-D
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DA, checkArgs=[basename, False]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, False]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"noPK/"+basename+".jar3dC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, False]))
......@@ -1026,7 +1026,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DB, checkArgs=[basename, True]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DC, checkArgs=[basename, True]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--jar3dcsv", outputDir+basename+".sites.csv", "-o", outputDir+"PK/"+basename+".jar3dD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUJAR3DD, checkArgs=[basename, True]))
# # bmotinBGSUBayesPairA-D
# # biorseoBGSUBayesPairA-D
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairA, checkArgs=[basename, False]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, False]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"noPK/"+basename+".bgsubypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, False]))
......@@ -1035,7 +1035,7 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypB", "--type", "B"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairB, checkArgs=[basename, True]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypC", "--type", "C"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairC, checkArgs=[basename, True]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".bgsubyp.csv", "-o", outputDir+"PK/"+basename+".bgsubypD", "--type", "D"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBGSUBayesPairD, checkArgs=[basename, True]))
# # bmotinBayesPairA-D
# # biorseoBayesPairA-D
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypA", "--type", "A", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairA, checkArgs=[basename, False]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypB", "--type", "B", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairB, checkArgs=[basename, False]))
# joblist.append(Job(command=[biorseoDir+"/bin/biorseo", "-s", outputDir+basename+".fa", "--bayespaircsv", outputDir+basename+".byp.csv", "-o", outputDir+"noPK/"+basename+".bypC", "--type", "C", "-n"], priority=4, timeout=3600, how_many_in_parallel=3, checkFunc=check_biorseoBayesPairC, checkArgs=[basename, False]))
......@@ -1088,13 +1088,15 @@ print("Loaded %d RNAs of length between 10 and 100. %d of them contain pseudokno
# print()
# for j in fails:
# print(j.cmd_)
# exit()
# else:
# print()
# print("Computations ran successfully.")
# print()
# ================= Statistics (without pseudoknots) ========================
print("Loading results from files... (without pseudoknots)")
# load results in objects
for instance in RNAcontainer:
instance.load_results_from(outputDir + "noPK/")
......@@ -1167,9 +1169,11 @@ print("==> %s ARN were predicted with all methods successful." % is_all(len(x_no
test = stats.friedmanchisquare(*x_noPK_fully)
print("Friedman test without PK: H0 = 'The position parameter of all distributions is equal', p-value = ", test.pvalue)
# ==> No they are not, but none does better, no need to test one further.
print()
# ================= Statistics (with pseudoknots) ========================
print("Loading results from files... (with pseudoknots)")
# load results in objects
for instance in RNAcontainer:
instance.load_results_from(outputDir + "PK/")
......@@ -1260,32 +1264,32 @@ test = stats.wilcoxon(x_PK_fully[0], x_PK_fully[11])
print("Wilcoxon signed rank test with PK: H0 = 'The position parameter of Biokop and Jar3dD are equal', p-value = ", test.pvalue)
# ================== Print results for application cases =====================
labels = ["Biokop","Biokop","RawA","RawB","BayesPairingA","BayesPairingB","BayesPairingC","BayesPairingD","JAR3DA","JAR3DB","JAR3DC","JAR3DD","BGSUBayesPairingA","BGSUBayesPairingB","BGSUBayesPairingC","BGSUBayesPairingD"]
print("RNAsubopt",":",x_noPK[0])
print("RNA-MOIP",":",x_noPK[1])
for data, name in zip(x_PK, labels):
print(name,":",data)
labels = ["RNAsubopt","Biokop\t", "RNA MoIP\t","RawA\t","RawB\t","BayesPairingA","BayesPairingB","BayesPairingC","BayesPairingD","JAR3DA\t","JAR3DB\t","JAR3DC\t","JAR3DD\t","BGSUBPairingA","BGSUBPairingB","BGSUBPairingC","BGSUBPairingD"]
for r in RNAcontainer:
print("\n",r.header_,"\nTrue structure:\t", r.true2d)
for m, name in zip([r.rnasubopt, r.biokop, r.rnamoip,
r.biorseoRawA,
r.biorseoRawB,
r.biorseoBayesPairA,
r.biorseoBayesPairB,
r.biorseoBayesPairC,
r.biorseoBayesPairD,
r.biorseoBGSUJAR3DA,
r.biorseoBGSUJAR3DB,
r.biorseoBGSUJAR3DC,
r.biorseoBGSUJAR3DD,
r.biorseoBGSUBayesPairA,
r.biorseoBGSUBayesPairB,
r.biorseoBGSUBayesPairC,
r.biorseoBGSUBayesPairD ], labels):
print(name+":\t",m.best_pred)
# # ================== Print results for application cases =====================
# labels = ["Biokop","Biokop","RawA","RawB","BayesPairingA","BayesPairingB","BayesPairingC","BayesPairingD","JAR3DA","JAR3DB","JAR3DC","JAR3DD","BGSUBayesPairingA","BGSUBayesPairingB","BGSUBayesPairingC","BGSUBayesPairingD"]
# print("RNAsubopt",":",x_noPK[0])
# print("RNA-MOIP",":",x_noPK[1])
# for data, name in zip(x_PK, labels):
# print(name,":",data)
# labels = ["RNAsubopt","Biokop\t", "RNA MoIP\t","RawA\t","RawB\t","BayesPairingA","BayesPairingB","BayesPairingC","BayesPairingD","JAR3DA\t","JAR3DB\t","JAR3DC\t","JAR3DD\t","BGSUBPairingA","BGSUBPairingB","BGSUBPairingC","BGSUBPairingD"]
# for r in RNAcontainer:
# print("\n",r.header_,"\nTrue structure:\t", r.true2d)
# for m, name in zip([r.rnasubopt, r.biokop, r.rnamoip,
# r.biorseoRawA,
# r.biorseoRawB,
# r.biorseoBayesPairA,
# r.biorseoBayesPairB,
# r.biorseoBayesPairC,
# r.biorseoBayesPairD,
# r.biorseoBGSUJAR3DA,
# r.biorseoBGSUJAR3DB,
# r.biorseoBGSUJAR3DC,
# r.biorseoBGSUJAR3DD,
# r.biorseoBGSUBayesPairA,
# r.biorseoBGSUBayesPairB,
# r.biorseoBGSUBayesPairC,
# r.biorseoBGSUBayesPairD ], labels):
# print(name+":\t",m.best_pred)
# # ================= PLOTS OF RESULTS =======================================
......@@ -1356,10 +1360,10 @@ for r in RNAcontainer:
# # plt.axhline(y=0, color="black", linewidth=1)
# # plt.axhline(y=1, color="black", linewidth=1)
# plt.xticks([1.0+i for i in range(16)], labels[1:])
# plt.ylim((0, 1.01))
# plt.ylim((0.5, 1.01))
# plt.ylabel("MCC", fontsize=12)
# plt.subplots_adjust(left=0.05, right=0.95)
# # plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0]))
# plt.title("Performance without pseudoknots (%d RNAs included)" % len(x_noPK_fully[0]))
# ax = plt.subplot(212)
......@@ -1378,38 +1382,39 @@ for r in RNAcontainer:
# # plt.axhline(y=0, color="black", linewidth=1)
# # plt.axhline(y=1, color="black", linewidth=1)
# plt.xticks([1.0+i for i in range(16)], labels)
# plt.ylim((0, 1.01))
# plt.ylim((0.5, 1.01))
# plt.ylabel("MCC", fontsize=12)
# plt.subplots_adjust(left=0.05, right=0.95)
# # plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12)
# plt.text(6.2,-0.3,"Performance with pseudoknots (%d RNAs included)" % len(x_PK_fully[0]), fontsize=12)
# plt.show()
# # ================== MCC performance ====================================
# # plt.subplot(141)
# x = [
# [ rna.rnasubopt.max_mcc for rna in RNAs_fully_predicted],
# # [ rna.rnamoip.max_mcc for rna in RNAs_fully_predicted],
# [ rna.biorseoRawA.max_mcc for rna in RNAs_fully_predicted],
# # [ rna.biorseoRawB.max_mcc for rna in RNAs_fully_predicted],
# [ rna.biokop.max_mcc for rna in RNAs_fully_predicted],
# [ rna.biorseoBGSUJAR3DA.max_mcc for rna in RNAs_fully_predicted]
# ]
# colors = ['xkcd:blue','xkcd:red', 'green', 'cyan']
# labels = ["Best RNAsubopt prediction", "Best RawA prediction", "Best Biokop prediction", "Best JAR3DA prediction"]
# for y, col, lab in zip(x, colors, labels):
# x_data = [ i for i in range(len(y)) if y[i]]
# y_data = [ i for i in y if i]
# plt.scatter(x_data, y_data, color=col, label=lab, marker='o', s=2.5)
# plt.axhline(y=0, color='black', linewidth=1)
# plt.axvline(x=0, color='black', linewidth=1)
# plt.xlabel("RNA Strand verified tRNA structures (10 < |nt| < 100)")
# ================== MCC performance ====================================
RNAcontainer.sort(key=lambda x: x.rnasubopt.max_mcc)
x = [
[ rna.rnasubopt.max_mcc for rna in RNAcontainer],
[ rna.rnamoip.max_mcc for rna in RNAcontainer],
# [ rna.biorseoRawA.max_mcc for rna in RNAs_fully_predicted],
# [ rna.biorseoRawB.max_mcc for rna in RNAs_fully_predicted],
# [ rna.biokop.max_mcc for rna in RNAs_fully_predicted],
# [ rna.biorseoBGSUJAR3DA.max_mcc for rna in RNAs_fully_predicted]
]
colors = ['xkcd:blue','goldenrod']#xkcd:red', 'green', 'cyan']
labels = ["Best RNAsubopt MCC", "Best RNA-MoIP MCC"]# "Best RawA prediction", "Best Biokop prediction", "Best JAR3DA prediction"]
for y, col, lab in zip(x, colors, labels):
x_data = [ i for i in range(len(y)) if y[i]]
y_data = [ i for i in y if i]
plt.scatter(x_data, y_data, color=col, label=lab, marker='o', s=2.5)
plt.axhline(y=0, color='black', linewidth=1)
plt.axvline(x=0, color='black', linewidth=1)
# plt.xlabel("608 RNA structures structures (10 < |nt| < 100)")
# plt.ylabel("Mattews Correlation Coefficient")
# plt.title("Performance of the prediction method")
# plt.legend(loc="lower right")
# plt.show()
plt.title("Performance of the prediction method")
plt.legend(loc="upper left")
plt.show()
......