Threading by query batch for rpsblast/rpstblastn works for BLAST'ing large numbers of queries. Details on the information collected, how it is used, how to opt-out, and our Privacy statement is found here: Usage reporting - Help improve BLAST by sharing limited information about your search. This version supports a new usage reporting service and a new multi-theading feature. New Columns added to the Description Table. See the new manual on GitHub for information about setting up and running IgBLAST. IgBLAST 1.17 is available for download from the BLAST FTP area. 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. Previously, a sequence is considered to be productive if the V(D)J rearrangement frame is in-frame and no stop codon is found. Updated the definition for whether a sequence is productive or not to reflect this new field. 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.Ģ. 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. 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. Fixed phiblast core dump when -subject option is used.update_ now reports the database timestamp in ISO8601 format.update_ now supports the "-showall pretty" option for databases hosted at the NCBI.The number of SMP files included in a volume can be controlled with the new -new_smp_vol option. Makeprofiledb creates multiple volumes for a CDD database, which allows RPSBLAST to handle a larger number of records.Makeblastdb requires less virtual memory for smaller databases.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.This release provides full support for these GI's that will appear in nucleotide databases later this year. NOTE: The NCBI is preparing to use a larger numerical range for its GI identifier. These changes also allow us to support a different threading model (“threading by query”) that can be more efficient in some situations. We have made some improvements to how BLAST multi-threads and the amount of memory required by makeblastdb.įor this release, we have performed a major restructuring of the module that reads the BLAST databases.įor 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. See the release notes for more details at Rare problem with mutex that caused BLAST to crash.Makeblastdb will issue an error message and exit if it encounters a sequence longer than the maximum supported size (2,147,483,647 letters).Dustmasker has a new option to replace low complexity regions with N's (hard masking).Makeblastdb default volume size is now 3 billion bases (was 1 billion).TBLASTN can now handle database sequences up to 2 billion bases (was 1 billion).This makes BLAST databases more Findable in the FAIR sense. Makeblastdb now produces a (JSON) metadata file about the database.Blastn_vdb and tblastn_vdb included in the 2.13.0 release.Details on the information collected, how it is used, how to opt-out,Īnd our privacy statement is found here: New features Please let us know if you find any issues. These executables have passed our normal QA,īut this is our first release for this architecture. We have also produced ARM LINUX executables and placed them on the FTP site (ncbi-blast-2.13.0+-圆). See įor information on using these executables with WGS projects. Search SRA and WGS projects without the need to build a BLAST database. Starting with this release, we are including the blastn_vdb and tblastn_vdb executables in the BLAST+ distribution.
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