Tag: NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
RefSeq release 235 is now available online and from the FTP site! You can access RefSeq data through NCBI Datasets. The release is provided in several directories as a complete dataset and also as divided by logical groupings.
As of May 11, 2026, this full release incorporates genomic, transcript, and protein data containing:
Download release 19.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
Release 19.0 contains:
Continue reading “Now Available! NCBI Hidden Markov Models (HMM) Release 19.0”
Download release 18.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
Release 18.0 contains:
Continue reading “Now Available! NCBI Hidden Markov Models (HMM) Release 18.0”
As of December 2024, NCBI’s pilot tool, Read Assembly and Annotation Pipeline Tool (RAPT) will no longer be available.
We encourage you to check out NCBI’s suite of assembly and annotation tools including the genome assembler SKESA, the taxonomic assignment tool ANI, and the prokaryotic genome annotation pipeline (PGAP).
Follow us on social @NCBI and join our mailing list to keep up to date with NCBI news.
Feel free to contact our help desk at [email protected] if you have any questions or concerns.
Download release 16.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
Release 16.0 contains:
Continue reading “NCBI Hidden Markov Models (HMM) Release 16.0 Now Available!”
We are happy to announce the release of a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP).
Download release 15.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
Release 15.0 contains:
Continue reading “NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!”
Download release 14.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP)! Search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. Continue reading “Now Available: NCBI Hidden Markov Models (HMM) Release 14.0!”
Release 13.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available for download. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.
The 13.0 release contains:
Continue reading “NCBI Hidden Markov Models (HMM) Release 13.0 Now Available!”
We are happy to announce the release of a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP) with many exciting new features.
This version has an improved user interface that takes the genome FASTA file and associated organism name directly on the command line. For example, to annotate a Vibrio cholerae genome sequence in the file Vchol.fasta:
pgap.py -r -g Vchol.fasta -s 'Vibrio cholerae' -o Vchol.annot
For more details visit our Quick Start page. Continue reading “New! May 2023 Release of Stand-Alone PGAP”