BLAST (Basic Alignment Search Tool) is a heuristic derivation of the Needleman & Wunsch bioinformatics DNA and amino acid sequence alignment algorithm. While the BLAST algorithm is slightly less accurate/precise than the Needleman & Wunsch algorithm, it accomplishes the alignment tremendously faster.
There are many implementations of the BLAST algorithm for different purposes. The program implemented with Symphony is called blastall. It performs a variety of different ungapped local alignments and is maintained by the NCBI (National Centre for Biotechnology Information). It is the most general and widely used open-source version of BLAST. Blastall accepts a sequence of DNA or amino acids and aligns the sequence against a specified database. The result is the homology of the sequence against that database. Sequences will usually range from 100 to 400 elements, while databases can range from 50MB to 4GB in size. BLAST takes 2 seconds to align a 100-element sequence with a 500MB database on a standard 2007 model computer. An alignment of a 1000-element sequence against a 500MB database takes 4.5 seconds. [more...]
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Parallel BLAST implementation using Symphony
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