2023 BLAST NEWS

Fri, 28 Apr 2023

BLAST+ 2.14.0 is here!

BLASTP, BLASTX, and TBLASTN are faster than before.

We have made BLAST searches faster for proteins and translated DNA(BLASTP, BLASTX, and TBLASTN) faster by improving support for initial long words. This improvement helps us speed up the fast modes (e.g., using -task blastp-fast on the command-line).

In one example, a search of phage reads(_ERR7959948) against swissprot using “-task blastx-fast” was four times faster than the default search (4 hours vs. 16 hours). This query(_ERR7959948) has 2.2 million reads and 324.4 million bases.

We have also fixed a number of bugs and added some other improvements.

Check out the release notes.

Download BLAST+ 2.14.0.

Mon, 24 Apr 2023

Faster BLASTP and BLASTX searches on the web!

BLASTP and BLASTX performance has been improved on the web.

Improvements

We have improved the BLASTP (protein-protein) and BLASTX (DNA-protein) searches with better support for longer word-sizes. With this change, searches against nr run about 20% faster with faster speed improvements for smaller databases like ClusteredNR, UniProtKB/Swiss-Prot, or PDB. This new version of BLAST produces equivalent results, with the overwhelming majority of searches returning the same results as the previous version of BLASTP and BLASTX.

Questions or comments? Please write the BLAST help desk.

Checkout BLASTP and BLASTX on the BLAST web service.

Tue, 21 Mar 2023

IgBLAST 1.21.0 is now available!

The improvements in this latest version are available to both the command line and web IgBLAST users.

Improvements

  • Added gaps to all _alignments_aa fields (such as sequence_alignment_aa) to reflect gaps in nucleotide sequence alignment.

  • Added the new AIRR format field: sequence_aa. This is the direct translation (no gaps) of a nucleotide sequence using the reading frame determined by the nucleotide alignment to its closest germline V gene.

  • Added the new AIRR format field: d_frame. This is the D gene frame that is in-frame with the J gene coding frame. IgBLAST offers built-in IGHD gene frame support for mouse as defined by Ichihara Y et al (European Journal of Immunology Volume 19, Issue 10 p. 1849-1854). Users can use their own custom D gene definition with IgBLAST depending on their needs.

Download IgBLAST here https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST.

Checkout the IgBLAST GitHub page at https://ncbi.github.io/igblast/.

Mon, 09 Jan 2023

ElasticBLAST 1.0.0 is Now available!

ElasticBLAST version 1.0.0 has support for faster cheaper disks at AWS and better supports Kubernetes on GCP!

ElasticBLAST versions prior to version 1.0.0 will stop working on GCP after January 31, 2023.

This is because older versions of ElasticBLAST rely on version 1.21 of kubernetes, which will reach its end of life on the Google Kubernetes Engine on that date. Please upgrade your installation of ElasticBLAST to its latest version.

Improvements

Bug fixes

  • ElasticBLAST uses GCP’s recommended way of dealing with read/write persistent disk.

  • Long user names no longer cause errors in AWS.

  • Fixed error caused by APIs not being enabled in GCP.

Please checkout this bioRxiv paper: ElasticBLAST: Accelerating Sequence Search via Cloud Computing.