2021 BLAST NEWS¶
Mon, 01 Nov 2021¶
A new feature was added to the NCBI IgBLAST webpage¶
IgBLAST is now able to determine Ig isotypes.
We have added a new function to the NCBI IgBLAST webpage. Users can now search immunoglobulin (Ig) nucleotide sequences with the Constant region (C) gene database to determine the Ig isotypes including subtypes (IgM, IgG, IgA1, etc). The isotype information is reported in the rearrangement summary table.
Additionally the C gene region is displayed in the alignment section.
This feature is now available for human and mouse sequences with possible expansion to other organisms in the future.
Tue, 13 Jul 2021¶
BLAST+ 2.12.0 is here!¶
We have made some improvements to how BLAST multi-threads and the amount of memory required by makeblastdb.
For this release, we have performed a major restructuring of the module that reads the BLAST databases. For multithreaded searches, these changes reduce the number of mutex calls, result in the use of fewer file pointers, and reduce the number of calls to memory map. These changes also allow us to support a different threading model (“threading by query”) that can be more efficient in some situations. See https://www.ncbi.nlm.nih.gov/books/NBK571452 for more information.
The NCBI is preparing to use a larger numerical range for its GI identifier. This release provides full support for these GI’s that will appear in nucleotide databases later this year.
Threading by query batch (for BLASTN, BLASTP, BLASTX, RPSBLAST, and RPSTBLASTN) may more efficiently BLAST large numbers of queries, especially if the database is small or the search is limited by taxid. Use “-mt_mode 1” to enable this option.
Makeblastdb requires less virtual memory for smaller databases.-
Makeprofiledb creates multiple volumes for a CDD database, which allows RPSBLAST to handle a larger number of records. The number of SMP files included in a volume can be controlled with the new -new_smp_vol option.
update_blastdb.pl now supports the “-showall pretty” option for databases hosted at the NCBI.
update_blastdb.pl now reports the database timestamp in ISO8601 format.-
Fixed phiblast core dump when -subject option is used.-
Fixed memory leak in setup procedures.-
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, 23 Feb 2021¶
A new feature was added to Primer-BLAST.¶
We now offer the ability for user to run primer-blast from NCBI assembly page.
This new feature allows users to design primers using additional eukaryote genome database that are not offered on NCBI Primer-Blast page. To use this feature, simply click “Run Primer-BLAST” link in the right column on the NCBI assembly page. For more information, please go to: https://ncbiinsights.ncbi.nlm.nih.gov/2021/02/18/assembly/.
Thu, 14 Jan 2021¶
A new version IgBLAST (1.17) is here.¶
We’ve added a new field “V frame shift” to the IgBLAST output to indicate if there is an internal frame shift in the normal V gene translation frame.
IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences.
New field “V frame shift” to the IgBLAST output to indicate if there is an internal frame shift in the normal V gene translation frame. Such frame shifts can arise due to the nucleotide deletion/insertion events introduced by somatic mutations; they can be found in some pseudogenes in germline configuration.
Updated the definition for whether a sequence is productive or not to reflect this new field. Previously, a sequence is considered to be productive if the V(D)J rearrangement frame is in-frame and no stop codon is found. Now the definition for a productive sequence includes no internal frame shift in V gene, in addition to previous requirement of V(D)J rearrangement frame being in-frame and no stop codon.
IgBLAST 1.17 is available for download from the BLAST FTP area. See the new manual on GitHub for information about setting up and running IgBLAST.