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Basic Local Alignment Search Tool (BLAST)

The Basic Local Alignment Search Tool was designed to find sequences in a DNA or protein sequence database by searching the data directly rather than searching for words that describe the sequence data. The tool was first implemented at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi). BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to the sequence database and calculates the statistical significance of matches. BLAST can be used to locate a gene or protein of interest, to infer functional and evolutionary relationships between sequences, as well as help identify members of gene families.

The input sequence used to run the tool is the query. The matching sequences found in the database by the tool are called hits. If your query sequence is a protein, use BLASTP to compare its amino acid sequence to proteins in the database. If you are interested in finding many orthologs of a query DNA sequence, use BLASTX, which translates the nucleotide sequence in all six frames and compares the result to protein sequences in the database. If you want to find the data page for the exact sequence you entered, use the BLASTN tool, which will match the query nucleotide sequence with nucleotide sequences in the database. The small number of characters and the degeneracy of the genetic code causes BLASTN to find shorter regions of alignment than BLASTX will find with the same query.

The results of the BLAST search are returned in order by a score which is based on the length and quality of alignment between query and hit sequences. An E Value is also calculated, which is the probability that an alignment of the same length and quality would be returned if the searched database contained random sequences. The closer to zero the better.

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.