BLAST

Overview

BLAST: In bioinformatics, BLAST is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.

User Manual

Using

Use the module name blast to discover versions available and to load the application.

Multicore

Some of the suite of tools can be used across multicores. Look at the help for each command to identify what it can do. For example look at blastp -help for the -num_threads option.

Blast Database

ARCC has a version of the related BLAST database installed on Teton and WilidIirs that is configured so that blast knows where to look for it (so you don't have to worry about this).
Due to the reasonably dynamic nature of this database, ARCC does have a method to update this database on request.

Which Version of the Database?

According to the discussion here, there is no specific version since these are live databases. You can check dates using for example:

[]$ module load gcc/12.2.0 blast-plus/2.13.0
[]$ blastdbcmd -db $BLASTDB/nr -info | head
Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects
        372,811,526 sequences; 135,507,326,095 total residues
Date: Apr 14, 2021  12:42 AM    Longest sequence: 74,488 residues
BLASTDB Version: 5
Volumes:
        /pfs/tc1/udata/blastdb/db/nr.00
        /pfs/tc1/udata/blastdb/db/nr.01

[]$ blastdbcmd -db $BLASTDB/htgs -info | head
Database: Unfinished High Throughput Genomic Sequences; Sequences: phases 0,1 and 2
        176,930 sequences; 27,769,248,758 total bases
Date: Jul 29, 2018  4:58 PM     Longest sequence: 6,788,435 bases
BLASTDB Version: 4
Volumes:
        /pfs/tc1/udata/blastdb/db/htgs.00
        /pfs/tc1/udata/blastdb/db/htgs.01

Version: 2.6.10

Since the last update of the database, version 2.6.0 is no longer compatible with this database. If you try running blastp with this version, you will see the following error message:

BLAST Database error: Error: Not a valid version 4 database.

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