Tag: Protein Family Model
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).
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!”
We are happy to announce a new version of the stand-alone Prokaryotic Genome Annotation Pipeline (PGAP). This version helps you interpret your results by providing an estimate of the completeness and contamination of your PGAP-annotated genome assembly using CheckM.
CheckM uses the presence of a set of lineage-specific genes for the species provided or the species returned by the taxonomy check (–taxcheck, –auto-correct-tax). The higher the completeness and the lower the contamination, the better the assembly is! If contamination is a concern, please try FCS-GX, a highly sensitive tool for detecting foreign contaminants in prokaryotic and eukaryotic genome assemblies.
This new release also contains code changes that improve prediction of some long genes, especially in low complexity regions. And, as with every release, PGAP incorporates incremental improvements from expert curators of the Protein Family Model collection that increase the precision of PGAP’s structural and functional annotation.
Please try this new version and share your experience with us!
We are excited to announce two improvements to the Read assembly and Annotation Pipeline Tool (RAPT), which allows you to assemble genomic reads for bacterial or archaeal isolates and annotate their genes at the click of a button.
Now RAPT verifies the scientific name you provide with the reads, and corrects it as needed with the Average Nucleotide Identity (ANI) tool, which compares your genome to type strain assemblies in GenBank to place it in the taxonomic tree. So, even if you only have a rough idea of the species you have sequenced, input datasets tailored to your genome will be used for the annotation and you will get the best possible gene set from RAPT. Continue reading “New in RAPT: Better taxonomic assignment and GO annotation”
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!”
RefSeq prokaryotic genomes and proteins are now annotated with Gene Ontology (GO) terms. Over the years we have received many requests to add GO terms to the annotations we provide. We heard you!
We are embarking on this adventure and starting to place terms from the Biological Process, Molecular Function and Cellular Component ontologies to genomes and proteins we annotate with the Prokaryotic Genome Annotation Pipeline (PGAP). Because of the hierarchical nature of the Gene Ontologies, these annotations will help the comparison of gene content across genomes at variable levels of specificity and eventually allow GO term enrichment analysis. GO terms are now associated with coding sequence (CDS) features on newly-submitted genomes (See Figure 1). They will progressively appear on genomes that are already in RefSeq as these get reannotated (about once a year). We expect all RefSeq genomes to have some GO terms by the spring of 2023.
Continue reading “Bacterial and archaeal genomes with GO terms in RefSeq!”