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BLAST

The Basic Local Alignment Search Tool (BLAST) program is by far the most widely used program to align sequences (Altschul et al., 1990). BLAST trawls a database for sequences similar to your sequence (the "query" sequence) by using the two-step approach shown in the following slides.

The basic concept is that the higher the number of similar segments between two sequences, and the longer the length of similar segments, the less different the sequences are, and therefore the more genetically related (homologous) to one another they are likely to be.

For a more detailed coverage, see the tutorials available from NCBI at http://www.ncbi.nlm.nih.gov/Education/ .