2018 BLAST NEWS

Wed, 19 Dec 2018

BLAST+ 2.8.1 is released.

New databases, better performance.

This is the first production release to support the new BLAST database version (BLASTDBv5). This is a taxonomically aware version of the BLAST database that:

  1. Allows you to limit your search by taxonomy using information built into the BLAST databases.

  2. Has improved performance when limiting BLAST search with accessions.

  3. Can retrieve sequences by taxonomy from a BLAST database with blastdbcmd. There are additional enhancements.

  4. A new option (-subject_besthit) culls HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another HSP. This is an experimental option and is subject to change.

  5. Use of the -max_target_seqs option for formats 0-4 is allowed. The number of alignments and descriptions will be set to max_target_seqs.

  6. A warning is issued if -max_target_seqs is set to less than five.

There are also some bug fixes. See the release notes are at https://www.ncbi.nlm.nih.gov/books/NBK131777/

The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

New version 5 databases are at https://ftp.ncbi.nlm.nih.gov/blast/db/v5

Read more about the version 5 database at https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf.

Thu, 06 Dec 2018

IgBLAST version 1.12 available.

IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.

The new version increases the allowed distance between V gene end and J gene start positions (from 90 bp to 150 bp) as well as between V gene end and D gene start positions (from 55 bp to 120 bp) to accommodate extremely long VDJ junctions found in some antibodies. This version better supports the new AIRR Rearrangement Schema (https://docs.airr-community.org/en/latest/datarep/rearrangements.html). Also, it includes fixes for minor bugs found in previous versions.

The release notes are available at https://ncbi.github.io/igblast/rel/Release-notes.html

The new executables are available on the NCBI FTP site at https://ftp.ncbi.nlm.nih.gov/blast/executables/igblast/release/LATEST

IgBLAST facilitates the analysis of immunoglobulin and T cell<br>receptor variable domain sequences. Read more here: https://ncbi.github.io/igblast/ and here: https://www.ncbi.nlm.nih.gov/pubmed/23671333.

Wed, 17 Oct

Learn how to use BLAST.

See our collection of webinars and tutorials designed to help you.

  • Improved standalone BLAST database and programs: now with taxonomic information

  • Getting the most out of Web BLAST tabular format

  • Using BLAST well, How to maximize your search efforts

  • 5 teaching examples on how to use NCBI BLAST

Tue, 21 Aug 2018

A new version (1.4.0) of the BLAST RNA-seq mapping tool, Magic-BLAST, is now available.

​Magic-BLAST version 1.4.0 is released.

The new version provides an option for strand-specific alignments, improved mapping sensitivity, better alignments in presence of higher sequencing error rates, and better splice site detection in compositionally biased genomes.

The release notes are available at https://ncbi.github.io/magicblast/release/release.html

The new executables are available on the NCBI FTP site at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Read more here: https://ncbi.github.io/magicblast and read our Magic-BLAST paper here: https://www.biorxiv.org/content/early/2018/08/13/390013.

Tue, 31 Jul 2018

Introducing the BLAST widget - integrating your BLAST results into NCBI’s Genome Data Viewer!

Want to analyze your BLAST results in the context of a genome browser and compare those results against other genome assembly annotations? Introducing the Genome Data Viewer (GDV) and the BLAST widget.

We have good news! NCBI has been listening and is pleased to introduce the BLAST widget, a new browser feature that seamlessly integrates your BLAST results as a track within the GDV genome browser. This widget provides direct access, within GDV, to execute and manage BLAST queries (BLASTN, TBLASTN) aligned to specific assembly displayed in GDV.

Learn more about the BLAST widget by viewing a short introductory tutorial. Click here to learn more about GDV.

Fri, 18 May 2018

IgBLAST 1.9.0 released.

IgBLAST now supports AIRR rearrangement reports.

With an increasing amount of repertoire studies using next generation sequencing (NGS) technology to generate very large sets of Ig/TCR rearrangement analysis data, it became clear a common standard was needed for sequence analysis result. This drove the adaptive immune receptor repertoire (AIRR) community to develop the AIRR standard so they can easily share their data. Details on the standard https://docs.airr-community.org/en/latest/

This format is available on web IgBlast page as well as in standalone IgBlast tool (with the -outfmt 19 option).

The new release is available on https://ftp.ncbi.nlm.nih.gov/blast/executables/igblast/release/1.9.0, along with a new manual on GitHub https://ncbi.github.io/igblast/.

IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.

Mon, 07 May 2018

May 16 webinar.

Improved BLAST+ and BLAST databases: now with taxonomic information.

Find out about easier taxonomic limits in the latest BLAST+ release. Read more and sign up at https://ncbiinsights.ncbi.nlm.nih.gov/2018/05/07/may-16-webinar-improved-standalone-blast-databases-programs-taxonomic-information/.

Wed, 28 Mar 2018

BLAST+ 2.8.0-alpha released.

BLAST+ now has a better database.

We have made some recent enhancement to the BLAST+ applications that allow you to:

  1. Limit your search by taxonomy using information built into the BLAST databases.

  2. Improved performance when limiting BLAST search with accessions.

  3. Use blastdbcmd to retrieve sequences by taxonomy from a BLAST database.

We’ve introduced a new version of the BLAST databases (version 5) to support the items listed above.

The new executables are at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.8.0alpha/

Sample version 5 databases are at ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5

Read more about the version 5 database at ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf

The release notes are at https://www.ncbi.nlm.nih.gov/books/NBK131777/

This is an alpha release to allow users to test and comment on new features.

Tue, 16 Jan 2018

QuickBLASTP webinar video.

NCBI insights lists new videos that are available.

QuickBLASTP is a new way to search large sets of proteins quickly for the most similar matches.