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
• [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