BLAST
BLAST (Basic Local Alignment Search Tool) is a similarity search program developed by the research staff at NCBI/GenBank. It is available
as a free service over the internet which provides very fast, accurate, and
sensitive database searching. However, it does have some limitations.
BLAST, like FASTA, is a word based method. However, one major difference is
that BLAST requires a pre-formatted search database.
To avoid keeping a second copy of every database (several GIGABYTES of data), the RCR has chosen to run our BLAST
searches (the BLAST program in GCG) remotely at the NCBI (in Washington, DC).
The disadvantage is that service is unpredictable - occasionally taking up to
half an hour in the middle of the day.
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It is possible to create a local BLAST database of personal sequences.
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BLAST works in roughly the following way.
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It takes each word from the query sequence (3 amino acids or 11 nucleotides), and locates all similar words in the current test sequence.
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If similar words are found, BLAST tries to expand the alignment to the adjacent words (but it does not allow gaps).
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After all words are tested, a set of HSPs (High-scoring Segment Pairs) are
chosen for that database sequence. Several short, non-overlapping HSPs may be combined in a statistical test to create a larger, more significant
match.
The NCBI's BLAST Help Manual is available on the Web at:
http://www.ncbi.nlm.nih.gov/BLAST/blast_help.html
and the GCG Program Manual chapter on the GCG version of BLAST is at:
http://ranger.med.nyu.edu/rcr/gcg/blast.html
