KnownIssues.md 1.78 KB
Annotation and numbering issues
- 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)
- Some chains are not correctly renamed A in the produced separate files (e.g. 1d4r-B)
- [SOLVED] Filtered alignments are shorter than the number of alignment columns saved to the SQL table
- Chain names appear in triple in the FASTA header (e.g. 1d4r-B 1d4r-B 1d4r-B)
Technical running issues
- [SOLVED] Files produced by Docker containers are owned by root and require root permissions to be read
- [SOLVED] SQLite WAL files are not deleted properly
Known feature requests
- [DONE] Get filtered versions of the sequence alignments containing the 3D chains, publicly available for download
- [DONE] Get a consensus residue for each alignement column
- [DONE] Get an option to limit the number of cores
- [DONE] Move to SILVA LSU release 138.1
- [UPCOMING] Automated annotation of detected Recurrent Interaction Networks (RINs), see http://carnaval.lri.fr/ .
- [UPCOMING] Possibly, automated detection of HLs and ILs from the 3D Motif Atlas (BGSU). Maybe. Their own website already does the job.
- [UPCOMING] Weight sequences in alignment to give more importance to rarer sequences
- [UPCOMING] 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