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: