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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
  • [DONE] Move to SILVA LSU release 138.1
  • [UPCOMING] Automated annotation of detected Recurrent Interaction Networks (RINs), see .
  • [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