Tag: Prokaryotic genome annotation

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” →

Announcing RefSeq Release 206!

RefSeq Release 206 is now available. This release includes the following:

Updated human genome Annotation Release 109.20210514
Updated Annotation Release 109.20210514 is an update of NCBI Homo sapiens Annotation Release 109. The annotation report is available here. The annotation products are available in the sequence databases and on the FTP site.

Other new eukaryotic genome annotations
This release includes new annotations generated by NCBI’s eukaryotic genome annotation pipeline for 45 additional species, including: Continue reading “Announcing RefSeq Release 206!” →

Prokaryotic representative genomes update–over 900 new species!

We are happy to announce an updated bacterial and archaeal representative genome collection! We have selected 13,835 among 214,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 6% since December 2020. About 950 species are represented for the first time, 476 species are represented by a better assembly, and 170 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

Continue reading “Prokaryotic representative genomes update–over 900 new species!” →

May 19 Webinar: Using the new web RAPT service to assemble and annotate prokaryotic genomes

Join us on May 19, 2021 at 12PM eastern time to learn how to use the new RAPT pilot service to assemble and annotate public or private Illumina genomic reads sequenced from bacterial or archaeal isolates at the click of a button. RAPT consists of two major components, the genome assembler SKESA and the Prokaryotic Genome Annotation Pipeline (PGAP), and produces an annotated genome of quality comparable to RefSeq in a couple of hours.

Date and time: Wed, May 19, 2021 12:00 PM – 12:45 PM EDT
Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI webinars playlist on the NLM YouTube channel. You can learn about future webinars on the Webinars and Courses page.

NCBI at CSHL Biology of Genomes, May 11 – 14, 2021

NCBI staff will be presenting virtual posters at the Cold Spring Harbor Laboratory Biology of Genomes Meeting, May 11 -14, 2021. The posters will cover the following topics: 1) a cloud-ready suite of tools (PGAP, RAPT , and SKESA) for assembling and annotating prokaryotic genomes, 2) Datasets — a new set of services for downloading genome assemblies and annotations, and 3) updates on NCBI RefSeq eukaryotic genome annotation, and the Genome Data Viewer (GDV). Read more below for the full abstracts.

The virtual poster gallery opens Tuesday, May 11 at 9:00 a.m. with dedicated time for poster viewing and discussion at 1:00 to 2:00 p.m. through Slack each day. The poster gallery will be open for entire the conference and remain available for six weeks afterwards. Continue reading “NCBI at CSHL Biology of Genomes, May 11 – 14, 2021” →

Prokaryotic representative genomes updated — now over 13 thousand assemblies!

We have updated the bacterial and archaeal representative genome collection! The current collection contains over 13,000 assemblies selected from the 203,000 prokaryotic RefSeq assemblies to represent their respective species. The collection has increased by 11% since August 2020. We’ve included about 1,400 species for the first time, have used better assemblies for 1,177 species, and have removed 65 species because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We have also updated the Representative Genomes Database on the Microbial Nucleotide BLAST page as well as the RefSeq Representative Genome Database on basic nucleotide BLAST, to reflect these changes. Continue reading “Prokaryotic representative genomes updated — now over 13 thousand assemblies!” →