2020 BLAST NEWS

Tue, 17 Nov 2020

New Columns added to the Description Table.

A user driven enhancement to improve the BLAST solution.

Through the BLAST survey and user feedback we received multiple requests to add additional columns to the Description table. We have added Scientific Name, Common Name, Taxid, and Accession Length. We are adding Common Name and Accession Length to the default list displayed. Click ‘Select Columns’ or ‘Manage Columns’ to add or delete columns. Your preferences will be saved for your next visit to BLAST.
When you download, only the columns displayed will be saved.

Tue, 05 Nov 2020

A new version BLAST+ (2.11.0) is here.

This version supports a new usage reporting service and a new multi-theading feature.

Usage reporting - Help improve BLAST by sharing limited information about your search. Details on the information collected, how it is used, how to opt-out, and our Privacy statement is found here: https://www.ncbi.nlm.nih.gov/books/NBK563686/
Threading by query batch for rpsblast/rpstblastn works for BLAST’ing large numbers of queries. For large numbers of queries, use the -mt option to more efficiently multi-thread the search.

Bug fixes

  • Fix slowdown in TBLASTN searches run without composition-based statistics on long database sequences.

  • Remove necessity of a network connection for blast_formatter. This also speeds up blast_formatter if the database can be found locally.

  • A core dump for RPSBLAST and RPSTBLASTN has been fixed.

  • Makeblastdb for windows has been fixed to not require as much virtual memory and to not produce overly large LMDB files.

See the release notes for more details at https://www.ncbi.nlm.nih.gov/books/NBK131777/
The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

Tue, 13 Oct 2020

BLAST now supports the new RefSeq Select databases.

The RefSeq Select data-set consists of a representative or “Select” transcript for every protein-coding gene.

To apply these new databases, use the pull down selector with Standard Databases selected in BLASTn and BLASTp. These database are also available on FTP/GCP/AWS sites for BLAST+ and BLAST+Docker users.
For in-depth information on the contents of these database go to this site https://www.ncbi.nlm.nih.gov/refseq/refseq_select/

Tue, 29 Sep 2020

A new feature was added to Primer-BLAST.

We have added a new function to Primer-BLAST that helps users design primers common for a group of highly similar sequences.

Many users want to test if a gene is expressed but they don’t know or they don’t care which transcripts are expressed. However, they do want primers to cover all transcript variants. Additionally, some users would like to have primers to cover a group of highly related bacteria strains.
Given a group of highly similar sequences, Primer-BLAST attempts to generate primers that are common for all sequences in this group. To find such primers, it uses BLAST to align the longest sequence among the group to the rest to find common regions which are then used to limit the locations of primers. The longest sequence is also used as the representative template sequence.
See the NCBI Insights post for an example search and more details.

Thu, 10 Sep 2020

New BLAST Default Parameters and Search Limits.

To provide a more useful BLAST output, maximize performance, and to make search time more consistent, webBLAST is updating some of the default parameters and search limits.

As previously announced, we have just made the following changes:

  1. Expect Value default will be 0.05

  2. Max target sequences limit will be no more than 5,000

  3. Max query sequence size for BLASTn, blastx and tblastx and will be 1,000,000

  4. Max query sequence size for BLASTp and tblastn will be 100,000

  5. Max query/subject sequence size for blast2Sequences mode will be 10,000,000

If you have any questions or concerns, please email us at blast-help@ncbi.nlm.nih.gov

Thu, 18 June 2020

BLAST+ 2.10.1 is released – Fix for TBLASTN Multi-Threading issue.

This version supports pulling databases from our FTP site as well from cloud providers or our BLAST+Docker solution.

See the release notes for more details at: https://www.ncbi.nlm.nih.gov/books/NBK131777/
The new executables are at https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST

Mon, 03 Feb 2020

Search Betacoronavirus Database

We have created a new BLAST Betacoronavirus Database focused on the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences. For further detail please visit NCBI GenBank

Wed, 22 Jan 2020

A new version IgBLAST (1.15.0) is here.

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

Improvements are:

  1. Support for the new FWR4 annotation feature in the AIRR format, both in standard format and in the AIRR alignment format.

  2. The previous “-penalty” parameter was renamed as -V_penalty to be consistent with other IgBLAST penalty options.

  3. Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters.

  4. Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.

IgBLAST 1.15 is available for downloadhttps://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST/ from the BLAST FTP area. See the the new <manual on GitHub for information about setting up and running IgBLAST.