Have you tried BLAST+ (2.9.0) and version 5 BLAST databases (dbV5)?


We recently updated the version 5 BLAST protein databases, (dbV5), on our FTP site to be completely accession-based.  As we described in a previous post, this means they now contain the gi-less proteins from the  NCBI Pathogen Project and other high-throughput projects. The v5 databases are also compatible with proteins from PDB structures with multi-character chain identifiers and will include these as they become available in our other protein systems. Only the latest version of BLAST+ (2.9.0, download) will work with the updated v5 databases and allow you to access all of the most recent protein data. At the end of September 2019, we will stop updating the version 4 BLAST databases and offer the v5 databases as the default for download.

For more information on the new database version and BLAST+ (2.9.0), see the previous NCBI Insights article and the recording of our recent webinar.

New BLAST results to become the default view August 1, 2019


We have been offering the new BLAST results page (Figure 1) for you to try out since April and have been collecting your comments and feedback.   Thank you all for your input on this new results display.  Over 90% of your comments have been positive.   We have made several changes to the page that address issues or problems that you have pointed out and are also working on adding several additional features that you have suggested in future releases.

At this time, 96% of you who have tried the new page have kept it as your default results page.  We are planning to make the new page the default for everyone on August 1, 2019. We will still provide access to the old results for some time to allow people who have workflows or teaching materials to adjust to the new display.

Blast_resultsFigure 1. The New BLAST Results with filters directly on the page and a more concise tabbed output that includes the taxonomy report. 

Please view our video introduction to the new results to see highlights of the improved display. As always, we will continue to incorporate your feedback into the design and features on the new page, so please test it out and let us know what you think.

IgBLAST (1.14.0) is now available with several improvements


IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. We’ve released a new version (1.14.0) of IgBLAST with three new improvements / bug fixes:

  1. Adaptive Immune Receptor Repertoire (AIRR) format is more consistent with AIRR specs including changing undefined type (NON, N/A) to empty string, not appending “reversed” to sequence identifier when the query is in reversed orientation, and using standard locus names such as IGH, TRB instead of traditional VH, VB etc.
  2.  The logic for showing CDR3 end of TCR sequences is improved.
  3. The sequence identifier is restored in the case of no results in AIRR rearrangement format.

IgBLAST 1.12 is available for download from the BLAST FTP area.  See the the new manual on GitHub for information about setting up and running IgBLAST.

RefSeq release 94 with MANE and RefSeq Select markup, protein name evidence, and improved [Candida] auris assembly


RefSeq release 94 is now available through NCBI web services, FTP and through NCBI’s Entrez programming utilities, E-utilities.

This full release incorporates genomic, transcript, and protein data available, as of May 13, 2019 and contains 200,311,267 records, including 141,839,334 proteins, 26,534,602 RNAs, and sequences from 91,873 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings.

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Prokaryotic Genome Annotation Pipeline (PGAP) now produces results suitable for submission to GenBank


We are happy to announce that you can now submit your genome sequences annotated by  your own local copy of the standalone Prokaryotic Genome Annotation Pipeline (PGAP) to GenBank.

How does it work? Download PGAP from GitHub, provide some basic information and the FASTA sequences for your genome sequence, and run the pipeline on your own machine, compute farm or the cloud. PGAP will produce annotation consistent with NCBI’s internal PGAP. Submit the resulting annotated genome to GenBank through the genome submission portal, and get an accession back.

As with any other submitted assembly, PGAP-annotated genomes will be screened for foreign contaminants and vector sequences at submission.  Any annotated assemblies that don’t pass may need to be modified. We are developing an automated process to handle these edits!

We are also working on other  improvements to stand-alone PGAP such as a module for calculating Average Nucleotide Identity (ANI) to confirm the assembly’s taxonomic assignment. Stay tuned for new developments!

 

May 15, 2019 Webinar: Using taxonomic information and other improvements in standalone BLAST+ (2.9.0) and the v5 databases


Next Wednesday, May 15, 2019 at 11AM, NCBI staff will show you how to use the latest version of standalone BLAST+ (2.9.0) and the new accession-based DBv5 databases with built-in taxonomy information. You will learn how to limit searches to taxonomic groups and to retrieve sequences from the database by taxonomy without having to download an identifier list. You will also learn about additional improvements in the BLAST databases and programs that make them compatible with the new PDB identifiers and gi-less proteins from the Pathogen Detection Project.

Date and time: Wed, May 15, 2018 11:00 AM – 11:30 AM 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 YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Over 1 billion records in GenBank release 231


GenBank release 231.0 (4/19/2019) is now available on the NCBI FTP site. This release has 5.03 terabases and 1.54 billion records.

The release has 212,775,414 traditional records containing 321,680,566,570 base pairs of sequence data. There are also 993,732,214 WGS records containing 4,421,986,382,065 base pairs of sequence data, 311,247,136 bulk-oriented TSA records containing 277,118,019,688 base pairs of sequence data, and 24,240,761 bulk-oriented TLS records containing 9,623,321,565 base pairs of sequence data.

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