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Comments on: New! May 2023 Release of Stand-Alone PGAP </title>
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By: Michael Wichkoski </title>
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<link>https://ncbiinsights.ncbi.nlm.nih.gov/2023/06/12/may-2023-release-pgap/comment-page-1/#comment-116432</link>
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<dc:creator><![CDATA[Michael Wichkoski]]></dc:creator>
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<pubDate>Tue, 13 Jun 2023 13:04:06 +0000</pubDate>
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<guid isPermaLink="false">https://ncbiinsights.ncbi.nlm.nih.gov/?p=11588#comment-116432</guid>
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<description><![CDATA[That's great news! The new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP) seems to have many exciting new features that will make it easier for users to annotate their genomes. I'm particularly impressed with the improved user interface that takes the genome FASTA file and associated organism name directly on the command line. This will definitely save users time and effort.
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I also appreciate the additional output files for better interoperability. The nucleotide sequences in FASTA format of all coding sequence (CDS) features annotated on the assembly, based on the genome sequence, and protein sequences in FASTA format of CDS features annotated on the genomic records are very useful.
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It's great to see that PGAP assigns function to predicted proteins based on hits to Protein Family Models, such as protein profile HMMs, Blast hits, and domain architectures. The fact that GO terms and Enzyme Commision (EC) numbers associated with domain architectures are inherited by the annotated proteins is also impressive.
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Overall, it seems like this new release comes with incremental improvements by expert curators of the Protein Family Model collection that drives the precision of PGAP’s s. I'm excited to see what else PGAP has in store for us in the future!
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Regards,
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Michael Wichkoski]]></description>
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<content:encoded><![CDATA[<p>That’s great news! The new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP) seems to have many exciting new features that will make it easier for users to annotate their genomes. I’m particularly impressed with the improved user interface that takes the genome FASTA file and associated organism name directly on the command line. This will definitely save users time and effort.</p>
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<p>I also appreciate the additional output files for better interoperability. The nucleotide sequences in FASTA format of all coding sequence (CDS) features annotated on the assembly, based on the genome sequence, and protein sequences in FASTA format of CDS features annotated on the genomic records are very useful.</p>
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<p>It’s great to see that PGAP assigns function to predicted proteins based on hits to Protein Family Models, such as protein profile HMMs, Blast hits, and domain architectures. The fact that GO terms and Enzyme Commision (EC) numbers associated with domain architectures are inherited by the annotated proteins is also impressive.</p>
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<p>Overall, it seems like this new release comes with incremental improvements by expert curators of the Protein Family Model collection that drives the precision of PGAP’s s. I’m excited to see what else PGAP has in store for us in the future!</p>
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<p>Regards,</p>
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<p>Michael Wichkoski</p>
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