Louis BECQUEY / RNANet

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Louis BECQUEY
511a1a19 1 parent 672867a8

Splitted Aglaé's code in a separate stats file

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...@@ -7,6 +7,15 @@ In `cmalign` alignments, - means a nucleotide is missing compared to the covaria ...@@ -7,6 +7,15 @@ In `cmalign` alignments, - means a nucleotide is missing compared to the covaria
7 7
8 In the final filtered alignment that we provide for download, the same rule applies, but on top of that, some '.' are replaced by '-' when a gap in the 3D structure (a missing, unresolved nucleotide) is mapped to an insertion gap. 8 In the final filtered alignment that we provide for download, the same rule applies, but on top of that, some '.' are replaced by '-' when a gap in the 3D structure (a missing, unresolved nucleotide) is mapped to an insertion gap.
9 9
10 +* **What are the cmalign options for ?**
11 +
12 +From Infernal's user guide, we can quote that Infernal uses an HMM banding technique to accelerate alignment by default. It also takes care of 3' or 5' truncated sequences to be aligned correctly (and we have some).
13 +First, one can choose an algorithm, between `--optacc` (maximizing posterior probabilities, the default) and `--cyk` (maximizing likelihood).
14 +
15 +Then, the use of bands allows faster and more memory efficient computation, at the price of the guarantee of determining the optimal alignment. Bands can be disabled using the `--nonbanded` option. A best idea would be to control the threshold of probability mass to be considered negligible during HMM band calculation with the `--tau` parameter. Higher values of Tau yield greater speedups and lower memory usage, but a greater chance to miss the optimal alignment. In practice, the algorithm explores several Tau values (increasing it by a factor 2.0 from the original `--tau` value) until the DP matrix size falls below the threshold given by `--mxsize` (default 1028 Mb) or the value of `--maxtau` is reached (in this case, the program fails). One can disable this exploration with option `--fixedtau`. The default value of `--tau` is 1e-7, the default `--maxtau` is 0.05. Basically, you may decide on a value of `--mxsize` by dividing your available RAM by the number of cores used with cmalign. If necessary, you may use less cores than you have, using option `--cpu`.
16 +
17 +Finally, if using `--cyk --nonbanded --notrunc --noprob`, one can use the `--small` option to align using the divide-and-conquer CYK algorithm from Eddy 2002, requiring a very few memory but a lot of time. The major drawback of this is that it requires `--notrunc` and `--noprob`, so we give up on the correct alignment of truncated sequences, and the computation of posterior probabilities.
18 +
10 * **Why are there some gap-only columns in the alignment ?** 19 * **Why are there some gap-only columns in the alignment ?**
11 20
12 These columns are not completely gap-only, they contain at least one dash-gap '-'. This means an actual, physical nucleotide which should exist in the 3D structure should be located there. The previous and following nucleotides are **not** contiguous in space in 3D. 21 These columns are not completely gap-only, they contain at least one dash-gap '-'. This means an actual, physical nucleotide which should exist in the 3D structure should be located there. The previous and following nucleotides are **not** contiguous in space in 3D.
...@@ -31,5 +40,5 @@ We first remove the nucleotides whose number is outside the family mapping (if a ...@@ -31,5 +40,5 @@ We first remove the nucleotides whose number is outside the family mapping (if a
31 40
32 * **What are the versions of the dependencies you use ?** 41 * **What are the versions of the dependencies you use ?**
33 42
34 -`cmalign` is v1.1.4, `sina` is v1.6.0, `x3dna-dssr` is v1.9.9, Biopython is v1.78. 43 +`cmalign` is v1.1.4, `sina` is v1.6.0, `x3dna-dssr` is v2.3.2-2021jun29, Biopython is v1.78.
35 44
...\ No newline at end of file ...\ No newline at end of file
......
...@@ -6,23 +6,16 @@ ...@@ -6,23 +6,16 @@
6 * Some chains are not correctly renamed A in the produced separate files (e.g. 1d4r-B) 6 * Some chains are not correctly renamed A in the produced separate files (e.g. 1d4r-B)
7 7
8 ## Alignment issues 8 ## Alignment issues
9 -* [SOLVED] Filtered alignments are shorter than the number of alignment columns saved to the SQL table `align_column`
10 * Chain names appear in triple in the FASTA header (e.g. 1d4r[1]-B 1d4r[1]-B 1d4r[1]-B) 9 * Chain names appear in triple in the FASTA header (e.g. 1d4r[1]-B 1d4r[1]-B 1d4r[1]-B)
11 10
12 -## Technical running issues
13 -* [SOLVED] Files produced by Docker containers are owned by root and require root permissions to be read
14 -* [SOLVED] SQLite WAL files are not deleted properly
15 -
16 # Known feature requests 11 # Known feature requests
17 -* [DONE] Get filtered versions of the sequence alignments containing the 3D chains, publicly available for download 12 +* Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
18 -* [DONE] Get a consensus residue for each alignement column 13 +* Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
19 -* [DONE] Get an option to limit the number of cores 14 +* Weight sequences in alignment to give more importance to rarer sequences
20 -* [DONE] Move to SILVA LSU release 138.1 15 +* Give both gap_percent and insertion_gap_percent
21 -* [UPCOMING] Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
22 -* [UPCOMING] Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
23 -* [UPCOMING] Weight sequences in alignment to give more importance to rarer sequences
24 -* [UPCOMING] Give both gap_percent and insertion_gap_percent
25 * A field estimating the quality of the sequence alignment in table family. 16 * A field estimating the quality of the sequence alignment in table family.
26 * Possibly, more metrics about the alignments coming from Infernal. 17 * Possibly, more metrics about the alignments coming from Infernal.
27 * Run cmscan ourselves from the NDB instead of using Rfam-PDB mappings ? (Iff this actually makes a real difference, untested yet) 18 * Run cmscan ourselves from the NDB instead of using Rfam-PDB mappings ? (Iff this actually makes a real difference, untested yet)
28 * Use and save Infernal alignment bounds and truncation information 19 * Use and save Infernal alignment bounds and truncation information
20 +* Save if a chain is a representative in BGSU list
21 +* Annotate unstructured regions (on a nucleotide basis)
......
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1 6ydp_1_AA_1176-2737 1 6ydp_1_AA_1176-2737
2 6ydw_1_AA_1176-2737 2 6ydw_1_AA_1176-2737
3 2z9q_1_A_1-72 3 2z9q_1_A_1-72
4 -1ml5_1_b_5-121
5 -1ml5_1_a_1-2914
6 3ep2_1_Y_1-72 4 3ep2_1_Y_1-72
7 3eq3_1_Y_1-72 5 3eq3_1_Y_1-72
8 4v48_1_A6_1-73 6 4v48_1_A6_1-73
9 -1ml5_1_A_2-1520 7 +1ml5_1_b_5-121
8 +1ml5_1_a_1-2914
10 1qzb_1_B_1-73 9 1qzb_1_B_1-73
11 1qza_1_B_1-73 10 1qza_1_B_1-73
12 1ls2_1_B_1-73 11 1ls2_1_B_1-73
12 +1ml5_1_A_2-1520
13 1gsg_1_T_1-72 13 1gsg_1_T_1-72
14 7d1a_1_A_805-902 14 7d1a_1_A_805-902
15 7d0g_1_A_805-913 15 7d0g_1_A_805-913
...@@ -22,15 +22,12 @@ ...@@ -22,15 +22,12 @@
22 2rdo_1_A_3-118 22 2rdo_1_A_3-118
23 4v48_1_A9_3-118 23 4v48_1_A9_3-118
24 4v47_1_A9_3-118 24 4v47_1_A9_3-118
25 +4v42_1_BA_1-2914
26 +4v42_1_BB_5-121
25 2ob7_1_A_10-319 27 2ob7_1_A_10-319
26 1x1l_1_A_1-130 28 1x1l_1_A_1-130
27 1zc8_1_Z_1-91 29 1zc8_1_Z_1-91
28 2ob7_1_D_1-130 30 2ob7_1_D_1-130
29 -4v42_1_BA_1-2914
30 -4v42_1_BB_5-121
31 -1r2x_1_C_1-58
32 -1r2w_1_C_1-58
33 -1eg0_1_L_1-56
34 3dg2_1_A_1-1542 31 3dg2_1_A_1-1542
35 3dg0_1_A_1-1542 32 3dg0_1_A_1-1542
36 4v48_1_BA_1-1543 33 4v48_1_BA_1-1543
...@@ -46,11 +43,14 @@ ...@@ -46,11 +43,14 @@
46 3dg4_1_B_1-2904 43 3dg4_1_B_1-2904
47 3dg5_1_B_1-2904 44 3dg5_1_B_1-2904
48 1eg0_1_O_1-73 45 1eg0_1_O_1-73
49 -1zc8_1_A_1-59 46 +1r2x_1_C_1-58
47 +1r2w_1_C_1-58
48 +1eg0_1_L_1-56
50 1jgq_1_A_2-1520 49 1jgq_1_A_2-1520
51 4v42_1_AA_2-1520 50 4v42_1_AA_2-1520
52 1jgo_1_A_2-1520 51 1jgo_1_A_2-1520
53 1jgp_1_A_2-1520 52 1jgp_1_A_2-1520
53 +1zc8_1_A_1-59
54 1mvr_1_D_1-59 54 1mvr_1_D_1-59
55 4c9d_1_D_29-1 55 4c9d_1_D_29-1
56 4c9d_1_C_29-1 56 4c9d_1_C_29-1
...@@ -61,12 +61,6 @@ ...@@ -61,12 +61,6 @@
61 3ep2_1_B_1-50 61 3ep2_1_B_1-50
62 3eq3_1_B_1-50 62 3eq3_1_B_1-50
63 3eq4_1_B_1-50 63 3eq4_1_B_1-50
64 -3pgw_1_R_1-164
65 -3pgw_1_N_1-164
66 -3cw1_1_x_1-138
67 -3cw1_1_w_1-138
68 -3cw1_1_V_1-138
69 -3cw1_1_v_1-138
70 2iy3_1_B_9-105 64 2iy3_1_B_9-105
71 3jcr_1_N_1-106 65 3jcr_1_N_1-106
72 2vaz_1_A_64-177 66 2vaz_1_A_64-177
...@@ -78,6 +72,12 @@ ...@@ -78,6 +72,12 @@
78 4v5z_1_BY_2-113 72 4v5z_1_BY_2-113
79 4v5z_1_BZ_1-70 73 4v5z_1_BZ_1-70
80 4v5z_1_B1_2-123 74 4v5z_1_B1_2-123
75 +3pgw_1_R_1-164
76 +3pgw_1_N_1-164
77 +3cw1_1_x_1-138
78 +3cw1_1_w_1-138
79 +3cw1_1_V_1-138
80 +3cw1_1_v_1-138
81 1mvr_1_B_1-96 81 1mvr_1_B_1-96
82 4adx_1_0_1-2923 82 4adx_1_0_1-2923
83 3eq4_1_Y_1-69 83 3eq4_1_Y_1-69
...@@ -295,7 +295,12 @@ ...@@ -295,7 +295,12 @@
295 6ucq_1_2Y 295 6ucq_1_2Y
296 4w2e_1_X 296 4w2e_1_X
297 6ucq_1_2X 297 6ucq_1_2X
298 +7n1p_1_DT
299 +7n2u_1_DT
298 6yss_1_W 300 6yss_1_W
301 +7n30_1_DT
302 +7n31_1_DT
303 +7n2c_1_DT
299 5afi_1_Y 304 5afi_1_Y
300 5uq8_1_Z 305 5uq8_1_Z
301 5wdt_1_Y 306 5wdt_1_Y
...@@ -333,6 +338,22 @@ ...@@ -333,6 +338,22 @@
333 4v4j_1_X 338 4v4j_1_X
334 4v4i_1_X 339 4v4i_1_X
335 4v42_1_BB 340 4v42_1_BB
341 +4jrc_1_B
342 +4jrc_1_A
343 +6lkq_1_S
344 +5h5u_1_H
345 +7d6z_1_F
346 +5lze_1_Y
347 +5lze_1_V
348 +5lze_1_X
349 +3jcj_1_G
350 +6o7k_1_G
351 +3dg2_1_A
352 +3dg0_1_A
353 +4v48_1_BA
354 +4v47_1_BA
355 +3dg4_1_A
356 +3dg5_1_A
336 6d30_1_C 357 6d30_1_C
337 6j7z_1_C 358 6j7z_1_C
338 3er9_1_D 359 3er9_1_D
...@@ -437,25 +458,22 @@ ...@@ -437,25 +458,22 @@
437 6doc_1_B 458 6doc_1_B
438 6doe_1_B 459 6doe_1_B
439 6n6g_1_D 460 6n6g_1_D
440 -6lkq_1_S
441 -5h5u_1_H
442 -7d6z_1_F
443 -5lze_1_Y
444 -5lze_1_V
445 -5lze_1_X
446 -3jcj_1_G
447 -6o7k_1_G
448 -3dg2_1_A
449 -3dg0_1_A
450 -4v48_1_BA
451 -4v47_1_BA
452 -3dg4_1_A
453 -3dg5_1_A
454 4b3r_1_W 461 4b3r_1_W
455 4b3t_1_W 462 4b3t_1_W
456 4b3s_1_W 463 4b3s_1_W
464 +7b5k_1_X
457 5o2r_1_X 465 5o2r_1_X
458 5kcs_1_1X 466 5kcs_1_1X
467 +7n1p_1_PT
468 +7n2u_1_PT
469 +7n30_1_PT
470 +7n31_1_PT
471 +7n2c_1_PT
472 +6yl5_1_I
473 +6yl5_1_E
474 +6yl5_1_A
475 +6yl5_1_K
476 +6yl5_1_G
459 6zvk_1_E2 477 6zvk_1_E2
460 6zvk_1_H2 478 6zvk_1_H2
461 7a01_1_E2 479 7a01_1_E2
...@@ -526,6 +544,7 @@ ...@@ -526,6 +544,7 @@
526 6w6l_1_V 544 6w6l_1_V
527 6olf_1_V 545 6olf_1_V
528 3erc_1_G 546 3erc_1_G
547 +4qjd_1_D
529 6of1_1_1W 548 6of1_1_1W
530 6cae_1_1Y 549 6cae_1_1Y
531 6o97_1_1W 550 6o97_1_1W
...@@ -557,7 +576,9 @@ ...@@ -557,7 +576,9 @@
557 4v48_1_A6 576 4v48_1_A6
558 2z9q_1_A 577 2z9q_1_A
559 4hot_1_X 578 4hot_1_X
579 +5ns4_1_C
560 6d2z_1_C 580 6d2z_1_C
581 +7eh0_1_I
561 4tu0_1_F 582 4tu0_1_F
562 4tu0_1_G 583 4tu0_1_G
563 6r9o_1_B 584 6r9o_1_B
...@@ -578,20 +599,23 @@ ...@@ -578,20 +599,23 @@
578 6sv4_1_NC 599 6sv4_1_NC
579 6i7o_1_NB 600 6i7o_1_NB
580 1ml5_1_A 601 1ml5_1_A
602 +7nsq_1_V
581 6swa_1_Q 603 6swa_1_Q
582 6swa_1_R 604 6swa_1_R
583 -3j6x_1_IR
584 -3j6y_1_IR
585 6ole_1_T 605 6ole_1_T
586 6om0_1_T 606 6om0_1_T
587 6oli_1_T 607 6oli_1_T
588 6om7_1_T 608 6om7_1_T
589 6olf_1_T 609 6olf_1_T
590 6w6l_1_T 610 6w6l_1_T
611 +6tnu_1_M
612 +5mc6_1_M
613 +7nrc_1_SM
591 6tb3_1_N 614 6tb3_1_N
592 7b7d_1_SM 615 7b7d_1_SM
593 7b7d_1_SN 616 7b7d_1_SN
594 6tnu_1_N 617 6tnu_1_N
618 +7nrc_1_SN
595 7nrd_1_SN 619 7nrd_1_SN
596 6zot_1_C 620 6zot_1_C
597 2uxb_1_X 621 2uxb_1_X
...@@ -602,6 +626,9 @@ ...@@ -602,6 +626,9 @@
602 1eg0_1_M 626 1eg0_1_M
603 3eq4_1_D 627 3eq4_1_D
604 5o1y_1_B 628 5o1y_1_B
629 +4kzy_1_I
630 +4kzz_1_I
631 +4kzx_1_I
605 3jcr_1_H 632 3jcr_1_H
606 6dzi_1_H 633 6dzi_1_H
607 5zeu_1_A 634 5zeu_1_A
...@@ -705,7 +732,6 @@ ...@@ -705,7 +732,6 @@
705 6ip6_1_ZZ 732 6ip6_1_ZZ
706 6uu3_1_333 733 6uu3_1_333
707 6uu1_1_333 734 6uu1_1_333
708 -1pn8_1_D
709 3er8_1_H 735 3er8_1_H
710 3er8_1_G 736 3er8_1_G
711 3er8_1_F 737 3er8_1_F
...@@ -744,9 +770,8 @@ ...@@ -744,9 +770,8 @@
744 4wtl_1_T 770 4wtl_1_T
745 4wtl_1_P 771 4wtl_1_P
746 1xnq_1_W 772 1xnq_1_W
747 -1x18_1_C 773 +7n2v_1_DT
748 -1x18_1_B 774 +4peh_1_Z
749 -1x18_1_D
750 1vq6_1_4 775 1vq6_1_4
751 4am3_1_D 776 4am3_1_D
752 4am3_1_H 777 4am3_1_H
...@@ -758,12 +783,45 @@ ...@@ -758,12 +783,45 @@
758 4wtj_1_T 783 4wtj_1_T
759 4wtj_1_P 784 4wtj_1_P
760 4xbf_1_D 785 4xbf_1_D
786 +5w1h_1_B
761 6n6d_1_D 787 6n6d_1_D
762 6n6k_1_C 788 6n6k_1_C
763 6n6k_1_D 789 6n6k_1_D
764 3rtj_1_D 790 3rtj_1_D
765 6ty9_1_M 791 6ty9_1_M
766 6tz1_1_N 792 6tz1_1_N
793 +6q1h_1_D
794 +6q1h_1_H
795 +6p7p_1_F
796 +6p7p_1_E
797 +6p7p_1_D
798 +6vm6_1_J
799 +6vm6_1_G
800 +6wan_1_K
801 +6wan_1_H
802 +6wan_1_G
803 +6wan_1_L
804 +6wan_1_I
805 +6ywo_1_F
806 +6wan_1_J
807 +4oau_1_A
808 +6ywo_1_E
809 +6ywo_1_K
810 +6vm6_1_I
811 +6vm6_1_H
812 +6ywo_1_I
813 +2a1r_1_C
814 +6m6v_1_F
815 +6m6v_1_E
816 +2a1r_1_D
817 +3gpq_1_E
818 +3gpq_1_F
819 +6o79_1_C
820 +6vm6_1_K
821 +6m6v_1_G
822 +6hyu_1_D
823 +1laj_1_R
824 +6ybv_1_K
767 6sce_1_B 825 6sce_1_B
768 6xl1_1_C 826 6xl1_1_C
769 6scf_1_I 827 6scf_1_I
...@@ -809,11 +867,12 @@ ...@@ -809,11 +867,12 @@
809 1y1y_1_P 867 1y1y_1_P
810 5zuu_1_I 868 5zuu_1_I
811 5zuu_1_G 869 5zuu_1_G
870 +7am2_1_R1
812 4peh_1_W 871 4peh_1_W
813 4peh_1_V 872 4peh_1_V
814 4peh_1_X 873 4peh_1_X
815 4peh_1_Y 874 4peh_1_Y
816 -4peh_1_Z 875 +7d8c_1_C
817 6mkn_1_W 876 6mkn_1_W
818 7kl3_1_B 877 7kl3_1_B
819 4cxg_1_C 878 4cxg_1_C
...@@ -826,14 +885,7 @@ ...@@ -826,14 +885,7 @@
826 4eya_1_F 885 4eya_1_F
827 4eya_1_Q 886 4eya_1_Q
828 4eya_1_R 887 4eya_1_R
829 -1qzc_1_B
830 -1t1o_1_B
831 1mvr_1_C 888 1mvr_1_C
832 -1t1m_1_B
833 -1t1o_1_C
834 -1t1m_1_A
835 -1t1o_1_A
836 -2r1g_1_B
837 4ht9_1_E 889 4ht9_1_E
838 6z1p_1_AB 890 6z1p_1_AB
839 6z1p_1_AA 891 6z1p_1_AA
...@@ -844,11 +896,9 @@ ...@@ -844,11 +896,9 @@
844 5uk4_1_W 896 5uk4_1_W
845 5uk4_1_U 897 5uk4_1_U
846 5f6c_1_E 898 5f6c_1_E
899 +7nwh_1_HH
847 4rcj_1_B 900 4rcj_1_B
848 1xnr_1_W 901 1xnr_1_W
849 -2agn_1_A
850 -2agn_1_C
851 -2agn_1_B
852 6e0o_1_C 902 6e0o_1_C
853 6o75_1_D 903 6o75_1_D
854 6o75_1_C 904 6o75_1_C
...@@ -866,8 +916,7 @@ ...@@ -866,8 +916,7 @@
866 1ibm_1_Z 916 1ibm_1_Z
867 4dr5_1_V 917 4dr5_1_V
868 4d61_1_J 918 4d61_1_J
869 -1trj_1_B 919 +7nwg_1_Q3
870 -1trj_1_C
871 5tbw_1_SR 920 5tbw_1_SR
872 6hhq_1_SR 921 6hhq_1_SR
873 6zvi_1_H 922 6zvi_1_H
...@@ -883,6 +932,8 @@ ...@@ -883,6 +932,8 @@
883 5k8h_1_A 932 5k8h_1_A
884 5z4a_1_B 933 5z4a_1_B
885 3jbu_1_V 934 3jbu_1_V
935 +4ts2_1_Y
936 +4ts0_1_Y
886 1h2c_1_R 937 1h2c_1_R
887 1h2d_1_S 938 1h2d_1_S
888 1h2d_1_R 939 1h2d_1_R
...@@ -909,6 +960,7 @@ ...@@ -909,6 +960,7 @@
909 6ppn_1_I 960 6ppn_1_I
910 5flx_1_Z 961 5flx_1_Z
911 6eri_1_AX 962 6eri_1_AX
963 +7k5l_1_R
912 7d80_1_Y 964 7d80_1_Y
913 1zc8_1_A 965 1zc8_1_A
914 1zc8_1_C 966 1zc8_1_C
...@@ -916,6 +968,7 @@ ...@@ -916,6 +968,7 @@
916 1zc8_1_G 968 1zc8_1_G
917 1zc8_1_I 969 1zc8_1_I
918 1zc8_1_H 970 1zc8_1_H
971 +6bfb_1_Y
919 1zc8_1_J 972 1zc8_1_J
920 7du2_1_R 973 7du2_1_R
921 4v8z_1_CX 974 4v8z_1_CX
...@@ -951,6 +1004,8 @@ ...@@ -951,6 +1004,8 @@
951 4x9e_1_H 1004 4x9e_1_H
952 6z1p_1_BB 1005 6z1p_1_BB
953 6z1p_1_BA 1006 6z1p_1_BA
1007 +3p22_1_C
1008 +3p22_1_G
954 2uxd_1_X 1009 2uxd_1_X
955 6ywe_1_BB 1010 6ywe_1_BB
956 3ol9_1_D 1011 3ol9_1_D
...@@ -973,8 +1028,6 @@ ...@@ -973,8 +1028,6 @@
973 3ol7_1_H 1028 3ol7_1_H
974 3ol8_1_L 1029 3ol8_1_L
975 3ol8_1_P 1030 3ol8_1_P
976 -1qzc_1_C
977 -1qzc_1_A
978 6yrq_1_E 1031 6yrq_1_E
979 6yrq_1_H 1032 6yrq_1_H
980 6yrq_1_G 1033 6yrq_1_G
...@@ -1054,6 +1107,7 @@ ...@@ -1054,6 +1107,7 @@
1054 3iy9_1_A 1107 3iy9_1_A
1055 4wtk_1_T 1108 4wtk_1_T
1056 4wtk_1_P 1109 4wtk_1_P
1110 +6wlj_3_A
1057 1vqn_1_4 1111 1vqn_1_4
1058 4oav_1_C 1112 4oav_1_C
1059 4oav_1_A 1113 4oav_1_A
...@@ -1070,18 +1124,13 @@ ...@@ -1070,18 +1124,13 @@
1070 3eq3_1_B 1124 3eq3_1_B
1071 3eq4_1_B 1125 3eq4_1_B
1072 4i67_1_B 1126 4i67_1_B
1073 -3pgw_1_R 1127 +4jf2_1_A
1074 -3pgw_1_N
1075 -3cw1_1_X
1076 -3cw1_1_W
1077 -3cw1_1_V
1078 -7b0y_1_A
1079 6k32_1_T 1128 6k32_1_T
1080 6k32_1_P 1129 6k32_1_P
1081 5mmj_1_A 1130 5mmj_1_A
1082 5x8r_1_A 1131 5x8r_1_A
1083 -2agn_1_E 1132 +3fu2_1_B
1084 -2agn_1_D 1133 +3fu2_1_A
1085 4v5z_1_BD 1134 4v5z_1_BD
1086 6yw5_1_AA 1135 6yw5_1_AA
1087 6ywe_1_AA 1136 6ywe_1_AA
...@@ -1117,6 +1166,17 @@ ...@@ -1117,6 +1166,17 @@
1117 3p6y_1_Q 1166 3p6y_1_Q
1118 3p6y_1_W 1167 3p6y_1_W
1119 5dto_1_B 1168 5dto_1_B
1169 +6yml_1_A
1170 +6ymm_1_A
1171 +6ymi_1_M
1172 +6ymi_1_F
1173 +6ymi_1_A
1174 +6ylb_1_F
1175 +6ymi_1_C
1176 +6ymj_1_C
1177 +6ylb_1_C
1178 +6ymj_1_I
1179 +6ymj_1_O
1120 4cxh_1_X 1180 4cxh_1_X
1121 1uvj_1_F 1181 1uvj_1_F
1122 1uvj_1_D 1182 1uvj_1_D
...@@ -1153,6 +1213,12 @@ ...@@ -1153,6 +1213,12 @@
1153 4v4f_1_B4 1213 4v4f_1_B4
1154 4v4f_1_A6 1214 4v4f_1_A6
1155 4v4f_1_B2 1215 4v4f_1_B2
1216 +7m4y_1_V
1217 +7m4x_1_V
1218 +6v3a_1_V
1219 +6v39_1_V
1220 +6ck5_1_A
1221 +6ck5_1_B
1156 5it9_1_I 1222 5it9_1_I
1157 7jqc_1_I 1223 7jqc_1_I
1158 5zsb_1_C 1224 5zsb_1_C
...@@ -1162,6 +1228,8 @@ ...@@ -1162,6 +1228,8 @@
1162 1cwp_1_D 1228 1cwp_1_D
1163 3jcr_1_N 1229 3jcr_1_N
1164 6gfw_1_R 1230 6gfw_1_R
1231 +3j6x_1_IR
1232 +3j6y_1_IR
1165 2vaz_1_A 1233 2vaz_1_A
1166 6zm6_1_X 1234 6zm6_1_X
1167 6zm5_1_X 1235 6zm5_1_X
...@@ -1177,11 +1245,11 @@ ...@@ -1177,11 +1245,11 @@
1177 5uh6_1_I 1245 5uh6_1_I
1178 6l74_1_I 1246 6l74_1_I
1179 5uh9_1_I 1247 5uh9_1_I
1248 +4v5z_1_BS
1180 2ftc_1_R 1249 2ftc_1_R
1181 7a5j_1_X 1250 7a5j_1_X
1182 6sag_1_R 1251 6sag_1_R
1183 4udv_1_R 1252 4udv_1_R
1184 -2r1g_1_E
1185 5zsc_1_D 1253 5zsc_1_D
1186 5zsc_1_C 1254 5zsc_1_C
1187 6woy_1_I 1255 6woy_1_I
...@@ -1209,7 +1277,7 @@ ...@@ -1209,7 +1277,7 @@
1209 3m85_1_X 1277 3m85_1_X
1210 3m85_1_Z 1278 3m85_1_Z
1211 3m85_1_Y 1279 3m85_1_Y
1212 -1e8s_1_C 1280 +5u34_1_B
1213 5wnp_1_B 1281 5wnp_1_B
1214 5wnv_1_B 1282 5wnv_1_B
1215 5yts_1_B 1283 5yts_1_B
...@@ -1232,8 +1300,11 @@ ...@@ -1232,8 +1300,11 @@
1232 6ij2_1_E 1300 6ij2_1_E
1233 3u2e_1_D 1301 3u2e_1_D
1234 3u2e_1_C 1302 3u2e_1_C
1303 +7eh1_1_I
1235 5uef_1_C 1304 5uef_1_C
1236 5uef_1_D 1305 5uef_1_D
1306 +7eh2_1_R
1307 +7eh2_1_I
1237 4x4u_1_H 1308 4x4u_1_H
1238 4afy_1_D 1309 4afy_1_D
1239 6oy5_1_I 1310 6oy5_1_I
...@@ -1244,13 +1315,15 @@ ...@@ -1244,13 +1315,15 @@
1244 6s0m_1_C 1315 6s0m_1_C
1245 6ymw_1_C 1316 6ymw_1_C
1246 7a5g_1_J 1317 7a5g_1_J
1318 +1m5k_1_B
1319 +1m5o_1_E
1320 +1m5v_1_B
1247 6gx6_1_B 1321 6gx6_1_B
1248 4k4s_1_D 1322 4k4s_1_D
1249 4k4s_1_H 1323 4k4s_1_H
1250 4k4t_1_H 1324 4k4t_1_H
1251 4k4t_1_D 1325 4k4t_1_D
1252 1zn1_1_C 1326 1zn1_1_C
1253 -1zn0_1_C
1254 1xpu_1_G 1327 1xpu_1_G
1255 1xpu_1_L 1328 1xpu_1_L
1256 1xpr_1_L 1329 1xpr_1_L
...@@ -1274,7 +1347,9 @@ ...@@ -1274,7 +1347,9 @@
1274 6gc5_1_F 1347 6gc5_1_F
1275 6gc5_1_H 1348 6gc5_1_H
1276 6gc5_1_G 1349 6gc5_1_G
1350 +4rne_1_C
1277 1n1h_1_B 1351 1n1h_1_B
1352 +7n2v_1_PT
1278 4ohz_1_B 1353 4ohz_1_B
1279 6t83_1_6B 1354 6t83_1_6B
1280 4gv6_1_C 1355 4gv6_1_C
...@@ -1290,6 +1365,9 @@ ...@@ -1290,6 +1365,9 @@
1290 4v5z_1_BC 1365 4v5z_1_BC
1291 5y88_1_X 1366 5y88_1_X
1292 4v5z_1_BB 1367 4v5z_1_BB
1368 +5y85_1_D
1369 +5y85_1_B
1370 +5y87_1_D
1293 3j0o_1_H 1371 3j0o_1_H
1294 3j0l_1_H 1372 3j0l_1_H
1295 3j0p_1_H 1373 3j0p_1_H
...@@ -1351,11 +1429,11 @@ ...@@ -1351,11 +1429,11 @@
1351 4e6b_1_A 1429 4e6b_1_A
1352 4e6b_1_B 1430 4e6b_1_B
1353 6a6l_1_D 1431 6a6l_1_D
1354 -4v5z_1_BS
1355 4v8t_1_1 1432 4v8t_1_1
1356 1uvi_1_D 1433 1uvi_1_D
1357 1uvi_1_F 1434 1uvi_1_F
1358 1uvi_1_E 1435 1uvi_1_E
1436 +3gs5_1_A
1359 4m7d_1_P 1437 4m7d_1_P
1360 4k4u_1_D 1438 4k4u_1_D
1361 4k4u_1_H 1439 4k4u_1_H
...@@ -1376,8 +1454,8 @@ ...@@ -1376,8 +1454,8 @@
1376 6ip5_1_2M 1454 6ip5_1_2M
1377 6ip6_1_2M 1455 6ip6_1_2M
1378 6qcs_1_M 1456 6qcs_1_M
1457 +7b5k_1_Z
1379 486d_1_G 1458 486d_1_G
1380 -2r1g_1_C
1381 486d_1_F 1459 486d_1_F
1382 4v5z_1_B0 1460 4v5z_1_B0
1383 4nia_1_O 1461 4nia_1_O
...@@ -1391,11 +1469,11 @@ ...@@ -1391,11 +1469,11 @@
1391 4oq9_1_F 1469 4oq9_1_F
1392 4oq9_1_L 1470 4oq9_1_L
1393 6r9q_1_B 1471 6r9q_1_B
1472 +7m4u_1_A
1394 6v3a_1_SN1 1473 6v3a_1_SN1
1395 6v3b_1_SN1 1474 6v3b_1_SN1
1396 6v39_1_SN1 1475 6v39_1_SN1
1397 6v3e_1_SN1 1476 6v3e_1_SN1
1398 -1pn7_1_C
1399 1mj1_1_Q 1477 1mj1_1_Q
1400 1mj1_1_R 1478 1mj1_1_R
1401 4dr6_1_V 1479 4dr6_1_V
...@@ -1437,14 +1515,25 @@ ...@@ -1437,14 +1515,25 @@
1437 6ow3_1_I 1515 6ow3_1_I
1438 6ovy_1_I 1516 6ovy_1_I
1439 6oy6_1_I 1517 6oy6_1_I
1440 -4bbl_1_Y
1441 -4bbl_1_Z
1442 4qvd_1_H 1518 4qvd_1_H
1443 5gxi_1_B 1519 5gxi_1_B
1444 3iy8_1_A 1520 3iy8_1_A
1445 -6tnu_1_M 1521 +7n06_1_G
1446 -5mc6_1_M 1522 +7n06_1_H
1523 +7n06_1_I
1524 +7n06_1_J
1525 +7n06_1_K
1526 +7n06_1_L
1527 +7n33_1_G
1528 +7n33_1_H
1529 +7n33_1_I
1530 +7n33_1_J
1531 +7n33_1_K
1532 +7n33_1_L
1447 5mc6_1_N 1533 5mc6_1_N
1534 +2qwy_1_C
1535 +2qwy_1_A
1536 +2qwy_1_B
1448 4eya_1_O 1537 4eya_1_O
1449 4eya_1_P 1538 4eya_1_P
1450 4eya_1_C 1539 4eya_1_C
...@@ -1453,8 +1542,6 @@ ...@@ -1453,8 +1542,6 @@
1453 6htq_1_W 1542 6htq_1_W
1454 6htq_1_U 1543 6htq_1_U
1455 6uu6_1_333 1544 6uu6_1_333
1456 -6v3a_1_V
1457 -6v39_1_V
1458 5a0v_1_F 1545 5a0v_1_F
1459 3avt_1_T 1546 3avt_1_T
1460 6d1v_1_C 1547 6d1v_1_C
...@@ -1497,6 +1584,7 @@ ...@@ -1497,6 +1584,7 @@
1497 6o78_1_E 1584 6o78_1_E
1498 6xa1_1_BV 1585 6xa1_1_BV
1499 6ha8_1_X 1586 6ha8_1_X
1587 +3bnp_1_B
1500 1m8w_1_E 1588 1m8w_1_E
1501 1m8w_1_F 1589 1m8w_1_F
1502 5udi_1_B 1590 5udi_1_B
...@@ -1520,16 +1608,29 @@ ...@@ -1520,16 +1608,29 @@
1520 6een_1_H 1608 6een_1_H
1521 4wti_1_T 1609 4wti_1_T
1522 4wti_1_P 1610 4wti_1_P
1611 +6dlr_1_A
1612 +6dlt_1_A
1613 +6dls_1_A
1614 +6dlq_1_A
1615 +6dnr_1_A
1523 5l3p_1_Y 1616 5l3p_1_Y
1524 4hor_1_X 1617 4hor_1_X
1525 3rzo_1_R 1618 3rzo_1_R
1619 +5wlh_1_B
1526 2f4v_1_Z 1620 2f4v_1_Z
1621 +5ml7_1_B
1527 1qln_1_R 1622 1qln_1_R
1623 +3pgw_1_R
1624 +3pgw_1_N
1625 +3cw1_1_X
1626 +3cw1_1_W
1627 +3cw1_1_V
1628 +7b0y_1_A
1528 6ogy_1_M 1629 6ogy_1_M
1529 6ogy_1_N 1630 6ogy_1_N
1530 6uej_1_B 1631 6uej_1_B
1632 +7kga_1_A
1531 6ywy_1_BB 1633 6ywy_1_BB
1532 -1x18_1_A
1533 5ytx_1_B 1634 5ytx_1_B
1534 4g0a_1_H 1635 4g0a_1_H
1535 6r9p_1_B 1636 6r9p_1_B
...@@ -1572,12 +1673,8 @@ ...@@ -1572,12 +1673,8 @@
1572 5mre_1_AA 1673 5mre_1_AA
1573 5mrf_1_AA 1674 5mrf_1_AA
1574 7jhy_1_Z 1675 7jhy_1_Z
1575 -2r1g_1_A
1576 -2r1g_1_D
1577 -2r1g_1_F
1578 3eq4_1_Y 1676 3eq4_1_Y
1579 4wkr_1_C 1677 4wkr_1_C
1580 -2r1g_1_X
1581 4v99_1_EC 1678 4v99_1_EC
1582 4v99_1_AC 1679 4v99_1_AC
1583 4v99_1_BH 1680 4v99_1_BH
...@@ -1641,44 +1738,21 @@ ...@@ -1641,44 +1738,21 @@
1641 6rcl_1_C 1738 6rcl_1_C
1642 5jju_1_C 1739 5jju_1_C
1643 4ejt_1_G 1740 4ejt_1_G
1741 +1et4_1_A
1742 +1et4_1_C
1743 +1et4_1_B
1744 +1et4_1_D
1745 +1et4_1_E
1746 +1ddy_1_C
1747 +1ddy_1_A
1748 +1ddy_1_E
1644 6lkq_1_W 1749 6lkq_1_W
1750 +6r47_1_A
1645 3qsu_1_P 1751 3qsu_1_P
1646 3qsu_1_R 1752 3qsu_1_R
1647 2xs7_1_B 1753 2xs7_1_B
1648 1n38_1_B 1754 1n38_1_B
1649 4qvc_1_G 1755 4qvc_1_G
1650 -6q1h_1_D
1651 -6q1h_1_H
1652 -6p7p_1_F
1653 -6p7p_1_E
1654 -6p7p_1_D
1655 -6vm6_1_J
1656 -6vm6_1_G
1657 -6wan_1_K
1658 -6wan_1_H
1659 -6wan_1_G
1660 -6wan_1_L
1661 -6wan_1_I
1662 -6ywo_1_F
1663 -6wan_1_J
1664 -4oau_1_A
1665 -6ywo_1_E
1666 -6ywo_1_K
1667 -6vm6_1_I
1668 -6vm6_1_H
1669 -6ywo_1_I
1670 -2a1r_1_C
1671 -6m6v_1_F
1672 -6m6v_1_E
1673 -2a1r_1_D
1674 -3gpq_1_E
1675 -3gpq_1_F
1676 -6o79_1_C
1677 -6vm6_1_K
1678 -6m6v_1_G
1679 -6hyu_1_D
1680 -1laj_1_R
1681 -6ybv_1_K
1682 6mpf_1_W 1756 6mpf_1_W
1683 6spc_1_A 1757 6spc_1_A
1684 6spe_1_A 1758 6spe_1_A
...@@ -1687,14 +1761,12 @@ ...@@ -1687,14 +1761,12 @@
1687 6fti_1_V 1761 6fti_1_V
1688 6ftj_1_V 1762 6ftj_1_V
1689 6ftg_1_V 1763 6ftg_1_V
1764 +3npn_1_A
1690 4g0a_1_G 1765 4g0a_1_G
1691 4g0a_1_F 1766 4g0a_1_F
1692 4g0a_1_E 1767 4g0a_1_E
1693 2b2d_1_S 1768 2b2d_1_S
1694 5hkc_1_C 1769 5hkc_1_C
1695 -4kzy_1_I
1696 -4kzz_1_I
1697 -4kzx_1_I
1698 1rmv_1_B 1770 1rmv_1_B
1699 4qu7_1_X 1771 4qu7_1_X
1700 4qu7_1_V 1772 4qu7_1_V
...@@ -1710,25 +1782,3 @@ ...@@ -1710,25 +1782,3 @@
1710 6pmi_1_3 1782 6pmi_1_3
1711 6pmj_1_3 1783 6pmj_1_3
1712 5hjz_1_C 1784 5hjz_1_C
1713 -7nrc_1_SM
1714 -7nrc_1_SN
1715 -7am2_1_R1
1716 -7k5l_1_R
1717 -7b5k_1_X
1718 -7d8c_1_C
1719 -7m4y_1_V
1720 -7m4x_1_V
1721 -7b5k_1_Z
1722 -7m4u_1_A
1723 -7n06_1_G
1724 -7n06_1_H
1725 -7n06_1_I
1726 -7n06_1_J
1727 -7n06_1_K
1728 -7n06_1_L
1729 -7n33_1_G
1730 -7n33_1_H
1731 -7n33_1_I
1732 -7n33_1_J
1733 -7n33_1_K
1734 -7n33_1_L
......
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