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

 

  • Bridges

  • BioU

 

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 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.

 

The BLAST programs are availiable through the Galaxy instance on BioU.

To make the BLAST programs availiable through the command line, type:

If you are using csh:

% source /packages/bin/SETUP_BIO_SOFTWARE

If you are using bash:

% source /packages/bin/SETUP_BIO_SOFTWARE

 

 

 See more help on BLAST.

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