Data: aa sequences are missing for some CDSs

[mshukla1]

AA sequences are missing for ~130,000 CDSs annotated by PATRIC. They belong to ~11,000 genomes in to total.

Actions:

• Add missing aa sequences
• Update corresponding faa files

[mshukla1]

After further analysis, it seems most of the CDSs missing AA sequences fall in one of the following categories:

• partial CDSs on the contig boundaries
• contain ambiguous bases
• correspond to pseudogenes in refseq annotations

All of the above situations result in erroneous translation resulting in uncommon start and/or premature stop codons. Hence, I decided not to populate those aa sequences in the database.

I have updated script that generate download files to exclude such features, to avoid fasta entries without sequences.

-Maulik

[mshukla1]

@olsonanl : we need to modify the annotation service to discard partial pegs/CDSs that can not be correctly translated.

[hyoo]

@mshukla1 @olsonanl Are we still working on this or this can be closed?