KnownIssues.md 1.57 KB
Annotation and numbering issues
- [SOLVED] Some GDPs that are listed as HETATMs in the mmCIF files are not detected correctly to be real nucleotides. (e.g. 1e8o-E)
- Some chains are truncated in different pieces with different chain names. Reason unknown (e.g. 6ztp-AX)
- [SOLVED] Some chains are not correctly renamed A in the produced separate files (e.g. 1d4r-B)
- [SOLVED] Chain names appear in triple in the FASTA header (e.g. 1d4r-B 1d4r-B 1d4r-B)
Known feature requests
- Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
- Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
- Weight sequences in alignment to give more importance to rarer sequences
- Give both gap_percent and insertion_gap_percent
- A field estimating the quality of the sequence alignment in table family.
- Possibly, more metrics about the alignments coming from Infernal.
- Run cmscan ourselves from the NDB instead of using Rfam-PDB mappings ? (Iff this actually makes a real difference, untested yet)
- Use and save Infernal alignment bounds and truncation information
- Save if a chain is a representative or not in BGSU list, so that they can be filtered easily
- Annotate unstructured regions (on a nucleotide basis)
Technical to-do list
cmalign --mergeis now deprecated, we use
esl-alimergeinstead. But, esl is a single-core process. We should run the merges of alignements of different families in parallel to save some time [TODO].