KnownIssues.md
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Known Issues
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)
Alignment issues
- [SOLVED] Filtered alignments are shorter than the number of alignment columns saved to the SQL table
align_column
- Chain names appear in triple in the FASTA header (e.g. 1d4r[1]-B 1d4r[1]-B 1d4r[1]-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
- [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.
- A field estimating the quality of the sequence alignment in table family.
- Possibly, more metrics about the alignments coming from Infernal.
- Move to SILVA LSU release 138