BLAST - Basic Local Alignment Search Tool

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.

To run this software interactively in a Linux environment run the commands:

module load ncbi_blast
blastall -p blastp -d swissprot -i my_seq.fa -o myblast.out

This sowftware will compare a protein sequence found in my_seq.fa against the swissprot protein database.

Local databases for BLAST searches are available in


Note:  Users are strongly encourage to use BLAST+, a new suite of BLAST tools with performance and feature improvements over the legacy BLAST applications.

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