We are happy to announce the release of a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP).
Tag: Hidden Markov Models (HMM)
NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!
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.
What’s New?
Release 15.0 contains:
- 16,667 HMMs maintained by NCBI
- 279 new HMMs since release 14.0
- Several hundreds HMMs with better names, EC numbers, Gene Ontology (GO) terms, gene symbols, or publications.
Continue reading “NCBI Hidden Markov Models (HMM) Release 15.0 Now Available!”
Now Available: NCBI Hidden Markov Models (HMM) Release 14.0!
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!”
NCBI Hidden Markov Models (HMM) Release 13.0 Now Available!
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.
What’s new?
The 13.0 release contains:
- 16,143 HMMs maintained by NCBI
- 315 new HMMs since release 12.0
- 286 HMMs with better names, EC numbers, Gene Ontology (GO) terms, gene symbols or publications
Continue reading “NCBI Hidden Markov Models (HMM) Release 13.0 Now Available!”
New! May 2023 Release of Stand-Alone PGAP
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.
Improved user interface
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”
NCBI Hidden Markov Models (HMM) Release 12.0 Now Available!
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.
What’s new?
The 12.0 release contains:
- 15,849 HMMs maintained by NCBI
- 271 new HMMs since release 11.0
- 1,248 HMMs with better names, EC numbers, Gene Ontology (GO) terms, gene symbols or publications
Continue reading “NCBI Hidden Markov Models (HMM) Release 12.0 Now Available!”
NCBI hidden Markov models (HMM) release 11.0 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!”
NCBI hidden Markov models (HMM) release 10.0 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.
NCBI hidden Markov models (HMM) release 8.0 now available!
Release 8.0 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 8.0 release contains 15,358 models, including 160 that are new since 7.0. In addition, we have added better names, EC numbers, Gene Ontology (GO) terms, gene symbols or publications to over 550 existing HMMs. 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 coding sequences and proteins annotated with PGAP. In case you missed it, see our previous blog post on this topic.
New version of PGAP available now!
We are happy to announce the release of a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP).
This version of PGAP offers a more streamlined experience to users who are uncertain about the taxonomic classification of the genomes they wish to annotate. Adding one flag to the command (--auto-correct-tax) results in the override of the species name provided on input if the taxonomy verification process predicts a different organism with high confidence. Continue reading “New version of PGAP available now!”