Category Archives: Gene Ontology (GO)
Gene Ontology (GO) Terms for NCBI RefSeq Eukaryotic Genomes
Are you interested in more functional information about protein-coding genes? We’ve expanded NCBI RefSeq’s Eukaryote Genome Annotation Pipeline (EGAP) to include Gene Ontology (GO) terms computed for most protein-coding genes. We are using the latest version of InterProScan, which now includes analysis based on PANTHER reference trees, on all NCBI RefSeq eukaryotic genomes. That means having … Continue reading Gene Ontology (GO) Terms for NCBI RefSeq Eukaryotic Genomes
Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records
Do you work with or study prokaryotic proteins? As previously announced, we’ve been adding Gene Ontology (GO) terms to RefSeq prokaryotic protein sequence records (example below) to standardize the language when describing the functions of genes and their products. Over 100 million RefSeq proteins from prokaryotes now have at least one GO Term, a 55% … Continue reading Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records
Posted by in Gene Ontology (GO), prokaryotes, Protein, RefSeq, What's New
Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records
Do you work with or study prokaryotic proteins? As previously announced, we’ve been adding Gene Ontology (GO) terms to RefSeq prokaryotic protein sequence records (example below) to standardize the language when describing the functions of genes and their products. Over 100 million RefSeq proteins from prokaryotes now have at least one GO Term, a 55% … Continue reading Gene Ontology (GO) Terms on 100M+ RefSeq Prokaryotic Protein Sequence Records
Posted by in Gene Ontology (GO), prokaryotes, Protein, RefSeq, What's New
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 … 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. The 11.0 release contains 15,643 HMMs maintained by NCBI, including 290 … 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 … Continue reading NCBI hidden Markov models (HMM) release 10.0 now available!
Announcing new links and annotations on Conserved Domain Search results!
Conserved Domain Search (CD Search) results now show domain architecture information and other annotations that further characterize predicted domain and protein function. These include links to PubMed, Gene Ontology (GO) terms, Enzyme Commission (EC) numbers, and the SPARCLE Domain Architecture Viewer. You can use these links on the results to find literature (PubMed), assign biological … Continue reading Announcing new links and annotations on Conserved Domain Search results!
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New in RAPT: Better taxonomic assignment and GO annotation
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. Improved taxonomic assignment Now RAPT verifies the scientific name you provide with the reads, and corrects it … Continue reading New in RAPT: Better taxonomic assignment and GO annotation
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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. … Continue reading NCBI hidden Markov models (HMM) release 8.0 now available!
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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 … Continue reading New version of PGAP available now!
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