Tag: NCBI Prokaryotic Genome Annotation Pipeline (PGAP)

RefSeq release 207 is available!

RefSeq release 207 is available!

RefSeq release 207 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 July 12, 2021, and contains 285,425,070 records, including 209,035,492 proteins, 39,039,901 RNAs, and sequences from 112,462 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. Continue reading “RefSeq release 207 is available!”

Announcing the re-annotation of RefSeq genome assemblies for E. coli and four other species!

We have re-annotated all RefSeq genomes for Escherichia coliMycobacterium tuberculosis, Bacillus subtilis, Acinetobacter pittii, and Campylobacter jejuni using the most recent release of PGAP. You will find that more genes now have gene symbols (e.g. recA). Your feedback indicated that the lack of symbols was an impediment to comparative analysis, so we hope that this improvement will help.

The number of re-annotated genomes is 25,619 for E. coli, 470 for B. subtilis, 6,828 for M. tuberculosis, 316 for A. pittii, and 1,829 for C. jejuni. On average, the increase in gene symbols is 30% in E. coli, 110% in B. subtilis, 57% in M. tuberculosis, 94% in A. pittii and 62% in C. jejuni (see Figure 1). After re-annotation, on average, 73% of PGAP-annotated E. coli genes and 79% of B. subtilis have symbols (35% for M. tuberculosis, 40% for A. pittii and 46% for C. jejuni). We assigned symbols to the annotated genes by calculating the orthologs between the genome of interest and the reference assembly for the species, and transferring the symbols from the reference genes to their orthologs in the annotated genomes.

Figure 1: Average and standard deviation of the number of genes annotated with symbols per genome, in the previous (blue) and the current annotation (orange). 

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New version of PGAP available now!

We are happy to announce that a new version of PGAP is available. This version will annotate 20 to 25% more genes with symbols (e.g. recA) on the assembled genomes of key species, compared to previous versions.

You will observe an increase in symbols when you annotate the genomes of Escherichia coli, Campylobacter jejuni and a few other species. As several users have requested, this feature will facilitate the comparison of gene content across multiple genomes. It is permitted by the addition of a new workflow to PGAP for identifying orthologs between the reference genomes of Escherichia coli str. K-12 substr. MG1655, Bacillus subtilis subsp. subtilis str. 168, Campylobacter jejuni subsp. jejuni NCTC 11168, Mycobacterium tuberculosis H37Rv, and Acinetobacter pittii PHEA-2 and genomes in the same species being annotated. Symbols of reference genes with defined function are propagated to their orthologs in the genome annotated with PGAP.

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Assemble and annotate your prokaryotic genomes with RAPT

Do you need an easy way to analyze a bacterium you just isolated? The latest version of NCBI’s Read assembly and Annotation Pipeline Tool (RAPT) is a pilot web service for the assembly and gene annotation of public or private Illumina genomic reads sequenced from bacterial or archaeal isolates.

We’ll be giving a webinar on webRAPT on May 19 where you can learn more, but you can test it out now.

Get started with the click of a button

RAPT is simple to use.

1. If you’re working with NIH’s Sequence Read Archive (SRA) and have an SRA accession, enter it in the first box below (Figure 1a) or upload a file of sequencing reads in the second box (Figure 1b).

screenshot of webRAPT submission; enter SRA accession number on the left or upload files on the right
Figure 1. 1a, on the left. Enter an SRA run accession (starting with SRR, DRR or ERR) in the text box on the left if you wish to assemble reads that are already public and press submit. If you are providing a read set that is not in SRA, use the box on the right, shown in 1b. Enter the organism name (genus only or genus species known to NCBI Taxonomy) in the “Organism” field. Click “One file” if all reads for the run are in a single file. This file can contain single-end reads or paired-end reads with reads of a pair adjacent to each other in the file (interleaved). Upload the sequencing reads using the “Choose file” button. Click “Two files” to provide forward and reverse reads from a paired-end library in two separate files. Upload the forward and reverse files using the “Choose Forward Reads File” and “Choose Reverse Reads File” buttons. Then press submit.



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

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 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”

Improvements to NCBI Assembly

NCBI’s genome Assembly has a number of significant improvements!

Assembly records now have a link to Primer-BLAST making it easy to design primers in the context of a specific eukaryote genome assembly.  Figure 1 shows the Assembly page for the Genome Reference Consortium Mouse Build 39 (GRCm39) with the link to Primer-BLAST.

Figure 1. The Assembly page for the mouse reference genome (GCF_000001635.27). Showing the new Run Primer-BLAST link, which loads the assembly as a database in the Primer-BLAST search (bottom) and the new expandable note sections, Genome-Annotation-Data in this case. 
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New release of the Read Assembly and Annotation Pipeline Tool (RAPT), now 2X faster!

There is a new release of the Read assembly and Annotation Pipeline Tool (RAPT) available from our GitHub site. RAPT is a one-step application for the genome assembly and gene annotation of archaeal and bacterial isolates that can run on your local computer or the Google Cloud Platform (GCP). With this new release, jobs will run twice as fast as with the December release. For example, we have assembled and annotated a Salmonella enterica genome in under an hour on a 16-CPU machine with the new release.
We have also added several new features based on your feedback including:

  1. The –stop-on-errors flag that will stop the process if there evidence from the average nucleotide identity check that there is sample mix-up or contamination by other bacteria.
  2. The ability to accept forward and reverse reads of paired-end runs in separate files. These can be compressed (gzip) files.

Finally, thanks to all who came to our webinar in December and provided their comments! For these who couldn’t join us, you can now view the recording on our YouTube channel.

Contact us at prokaryote-tools@ncbi.nlm.nih.gov with any question and to let us know if you would like to become a beta-tester for RAPT.

NCBI hidden Markov models (HMM) release 4.0 now available!

Release 4.0 of the NCBI hidden Markov models (HMM) used by the Prokaryotic Genome Annotation Pipeline (PGAP) is now available from our FTP site. You can search this collection against your favorite prokaryotic proteins to identify their function using the HMMER sequence analysis package.

This release contains 17,443 models, including 94 new models since the last release. We have also updated names and added EC numbers and  gene symbols to over 100 models. You can search and view the details of these HMMs in the newly deployed Protein Family Model collection that also includes conserved domain architectures and BlastRules  and allows you to find all RefSeq proteins named by these profiles. See our recent post for more details.

The Protein Family Model resource is now available!

The new Protein Family Model resource  (Figure 1) provides a way for you to search across the evidence used by the NCBI annotation pipelines to name and classify proteins. You can find protein families by gene symbol, protein function, and many other terms. You have access to related proteins in the family and publications describing members. Protein Family Models includes protein profile hidden Markov models (HMMs) and BlastRules for prokaryotes, and conserved domain architectures for prokaryotes and eukaryotes. The HMMs in the collection include Pfam models, TIGRFAMs as well as models developed at NCBI either de novo, or from NCBI protein clusters.  Each of the BlastRules (PMCID: 5753331) consists of one or more model proteins of known biological function with BLAST identity and coverage cutoffs.  The conserved domain architectures are based on BLAST-compatible Position Specific Score Matrices  (PSSMs) that constitute the NCBI Conserved Domain database.Figure 1. Protein Family Model resource pages. Top panel.  Home page. Middle  panel, selected results summaries from a fielded search for the DnaK gene product (DnaK[Gene Symbol]). Bottom panel, a portion of an HMM record for DnaK derived from NCBI Protein Clusters (NF009946). The record also includes PubMed citations and HMMER analyses showing the RefSeq proteins named by this method.

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