BLAST

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Documentation

  • Website: http://www.ncbi.nlm.nih.gov/books/NBK1762/
  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990)   “Basic local alignment search tool.”   J. Mol. Biol. 215:403-410.
  • Altschul, S.F., Madden, T.L., Sch###er, A.A., Zhang, J., Zhang, Z.,   Miller, W. & Lipman, D.J. (1997)   “Gapped BLAST and PSI-BLAST: a new generation of protein database   search programs.” Nucleic Acids Res. 25:3389-3402

Usage on Bridges-2

To see what versions of  BLAST are available and if there is more than one, which is the default, along with some help, type

module spider blast

To use BLAST, include a command like this in your batch script or interactive session to load the BLAST module: (note ‘module load’ is case-sensitive):

module load BLAST

Usage on Bridges

The BLAST database is available on Bridges.  After you load the BLAST module, use the BLASTDB environment variable in your job script or interactive session to access the BLAST databases.

To see what BLAST commands are available and how to get additional help, type

module help blast

To see what versions of BLAST are available, type

module avail blast

To use BLAST, include a command like this in your batch script or interactive session to load the BLAST module:

module load blast

When the BLAST module is loaded, an environment variable named $BLASTDB is set to point to the location of the NR database.

Be sure you also load any other modules needed, as listed by the module help blast command.

 See more help on BLAST.