Tag: Prokaryotic genome annotation

Updated bacterial and archaeal reference genomes collection now available!

An updated bacterial and archaeal reference genome collection is available! This collection of 17,163 genomes was built by selecting exactly one genome assembly for each species among the 272,000+ prokaryotic genomes in RefSeq, except for E. coli for which two assemblies were selected as reference.

A total of 497 species are included in this collection for the first time. In addition, comparing to the October 2022 set, 174 species are represented by a better assembly and 15 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment. The criteria for selecting one assembly for a given species from all assemblies available in RefSeq for the species include assembly contiguity and completeness and quality of the RefSeq annotation. See the documentation for details.

We have updated the nucleotide BLAST RefSeq reference genomes database (fourth in the menu) as well as the database on the Microbial Nucleotide BLAST page to reflect these changes. You can also run BLAST searches against the proteins annotated on these reference genomes (RefSeq Select proteins database, second in the menu).

Now available: Updated prokaryote representative genomes collection

An updated bacterial and archaeal representative genomes collection is available! We selected a total of 16,665 of the 262,000 prokaryotic assemblies in RefSeq to represent their respective species. For the first time, more complete assemblies (as calculated by CheckM) were ranked higher than less complete assemblies. See the ranked list of criteria for selecting representative assemblies here. Continue reading “Now available: Updated prokaryote representative genomes collection” →

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.

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 of our NCBI experts

“It was a great honor for me to receive the ASM Elizabeth O. King Lecturer Award. Thank you to my colleagues, without whom so much of my work would not have been possible, and to all of those who attended my presentation on Making Genomics Accessible to Aid Public Health and Research.”

~Michael Feldgarden, Ph.D. Continue reading “ASM Microbe 2022 was a success!” →

Announcing an updated prokaryotic representative genomes collection with 706 new species!

An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented by a better assembly, and 124 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative genomes database (fourth in the menu) to reflect these changes. Finally, remember that you can now run BLAST searches against the proteins annotated on representative genomes (second in the menu). See more info here.

Average Nucleotide Identity (ANI) for assembly validation

Validating genome assemblies submitted to GenBank using ANI based workflow

Average Nucleotide Identity (ANI) analysis is a useful tool to verify taxonomic identities in prokaryotic genomes. As part of the NCBI bacterial genome submission process, GenBank performs ANI analyses to compare submitted prokaryotic genome assemblies against reference data generated from type strains. You can learn about more about the relevant workflow and about type strain curation in our publications (PMC6978984 and PMC4383940).

We use genomes obtained from type strains (type assemblies) in computational comparisons, for example using ANI to reclassify or modify existing taxonomy with reasonable confidence. The taxonomy check status for all 1.3 million bacterial genome assemblies is summarized in the ANI_report_prokaryotes.txt file available from the ASSEMBLY_REPORTS FTP directory. The README file describes the contents of the report in detail. You can run ANI on your genome on its own or in the context of annotation. Find more information here. Continue reading “Average Nucleotide Identity (ANI) for assembly validation” →

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 models added to the NCBI Hidden Markov models (HMM) collection with release 7.0

Release 7.0 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.

Figure 1. Recently added HMM-based Protein Family Model for the histidine-histamine antiporter family (NF040512), with GO terms (framed in red).

Continue reading “New models added to the NCBI Hidden Markov models (HMM) collection with release 7.0” →

Updated prokaryotic representative genome collection

The bacterial and archaeal representative genome collection has been updated! We selected a total of 14,912 of the 224,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has grown by 8% since April 2021 and now includes Candidatus and endosymbiont species (Figure 1), which constitute 303 and 140 respectively of the 1,077 newly added species. In addition, 719 species are represented by a better assembly, and 70 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

Figure 1. Graphical view of a portion of the RefSeq Representative assembly for the bedbug endosymbiont Candidatus Wolbachia massiliensis isolate PL13.

Continue reading “Updated prokaryotic representative genome collection” →

Search the NCBI Hidden Markov models collection against your favorite prokaryotic proteins

The NCBI Hidden Markov models (HMM) 6.0 release, available on our FTP site, has 15,247 models supported at NCBI. We created 80 more new HMMs and consolidated the collection by removing 2,151 HMMs that were nearly identical to another. Release 6.0 also incorporates 12,656 PFAM from release 34 that apply to prokaryotic proteins. You can use the HMMER sequence analysis package to search the collection against your favorite prokaryotic proteins to identify their function. We have also added more specific names or associated EC number, gene symbols and publication to over 500 HMMs.

Gene Ontology (GO) term attributes are now available for 20% of HMM models (see Figure 1 below). We added most of these based on existing mappings, but our experts are working on creating more associations. Starting in the fall, we’ll start propagating GO terms from HMMs to annotated genomes and proteins!

**Figure 1.** Example Protein Family Model, TIGR03697.1 for the global nitrogen regulator NtcA protein family, with newly shown GO terms (framed in red).

Continue reading “Search the NCBI Hidden Markov models collection against your favorite prokaryotic proteins” →