Tag: Hidden Markov Models (HMM)
Download release 17.0 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 17.0 contains:
Continue reading “Now Available! NCBI Hidden Markov Models (HMM) Release 17.0”
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”
Release 12.0 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 12.0 release contains:
Continue reading “NCBI Hidden Markov Models (HMM) Release 12.0 Now Available!”
Release 11.0 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. Continue reading “NCBI hidden Markov models (HMM) release 11.0 now available!”
Release 10.0 of the NCBI Hidden Markov models (HMM) 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 10.0 release contains 15,360 models maintained by NCBI, including 228 that are new since 9.0, 99 that were modified significantly, and 205 that were assigned better names, EC numbers, Gene Ontology (GO) terms, gene symbols or publications. You can search and view the details for these in the Protein Family Model collection, which also includes conserved domain architectures and BlastRules, and find all RefSeq proteins they name.
GO terms associated with HMMs are now propagated to CDSs and proteins annotated with PGAP. In case you missed it, see our previous blog post on this topic.