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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.


  • 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

The BLAST databases are installed on Bridges-2 under /ocean/datasets/community/genomics/blast  and can be accessed with the environment variable $BLAST_DATABASE when the BLAST module has been loaded.

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

There are many search programs in the BLAST suite, depending on the  type of analysis to be done. For a list of what is included on Bridges-2, type

module help BLAST

To find the general usage of an individual program in the BLAST suite, use the -help flag. For example:

blastn -help