Category Archives: prokaryotes
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
RefSeq Release 216
RefSeq release 216 is now available online, from the FTP site, and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of January 9, 2023, and contains 342,395,932 records, including 249,868,639 proteins, 49,869,497 RNAs, and sequences from 128,299 organisms. The release is provided in several directories as a complete … Continue reading RefSeq Release 216
Prokaryotic phylum name changes coming soon!
Beginning in the first week of January 2023, NCBI Taxonomy will initiate changes to prokaryote phylum names in accordance with the recent inclusion of rank ‘phylum’ in the International Code of Nomenclature for Prokaryotes (ICNP). We first announced this update that involves changes to 42 NCBI taxa about a year ago. We will change several names … Continue reading Prokaryotic phylum name changes coming soon!
Posted by in NCBI Taxonomy, prokaryotes, What's New
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!
ASM Microbe 2022 was a success!
NCBI had the pleasure of attending and participating in this year’s American Society of Microbiology (ASM) Microbe conference, June 9-13 in Washington, D.C. NCBI staff participated in activities and events throughout the three-day conference. Over 4,500 attendees gathered in the exhibit hall and joined a variety of poster presentations and talks! Reflections from a few … Continue reading ASM Microbe 2022 was a success!
The post ASM Microbe 2022 was a success! appeared first on NCBI Insights.
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!
The post NCBI hidden Markov models (HMM) release 8.0 now available! appeared first on NCBI Insights.
Updated protein family models used by PGAP available for download
Release 3.0 of the NCBI protein family models used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available from our FTP site. You can search this collection of hidden Markov models (HMMs) against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package. The 3.0 release contains 17,350 models: 12,864 … Continue reading Updated protein family models used by PGAP available for download
Posted by in PGAP, prokaryotes, prokaryotic genome annotation, Protein, RefSeq, What's New
Enhanced prokaryote type strain report now with details on needed type strain data
The Prokaryote type strain report provides information on type-strains for over 18,000 species. We revised and expanded the report to make it easier to identify cases where sequencing or establishing type material would have the biggest impact on improving prokaryote taxonomy … Continue reading
Posted by in assembly, Genome, prokaryotes, taxonomy, What's New
Expanded average nucleotide identity analysis now available for prokaryotic genome assemblies
As we described in an earlier post, GenBank uses average nucleotide identity (ANI) analysis to find and correct misidentified prokaryotic genome assemblies. You can now access ANI data for the more than 600,000 GenBank bacterial and archaeal genome assemblies through … Continue reading
Posted by in assembly, Genbank, Genome, prokaryotes, taxonomy, What's New