We are happy to announce that a new version of PGAP is available. This version will annotate 20 to 25% more genes with symbols (e.g. recA) on the assembled genomes of key species, compared to previous versions.
You will observe an increase in symbols when you annotate the genomes of Escherichia coli, Campylobacter jejuni and a few other species. As several users have requested, this feature will facilitate the comparison of gene content across multiple genomes. It is permitted by the addition of a new workflow to PGAP for identifying orthologs between the reference genomes of Escherichia coli str. K-12 substr. MG1655, Bacillus subtilis subsp. subtilis str. 168, Campylobacter jejuni subsp. jejuni NCTC 11168, Mycobacterium tuberculosis H37Rv, and Acinetobacter pittii PHEA-2 and genomes in the same species being annotated. Symbols of reference genes with defined function are propagated to their orthologs in the genome annotated with PGAP.
This version of PGAP also comes with incremental improvements to the protein family model collection packaged with PGAP that drives accurate structural and functional annotation.
Try it and send us your feedback!