BLAST, the Basic Local Alignment Search Tool, searches a sequence database for high-scoring local similarities. It uses promising short matches to guide extension rather than exhaustively evaluating every possible alignment. Reported scores and expected counts help evaluate matches under a background model; they do not directly establish common function. A short conserved domain can produce a strong local match even when the complete proteins have different overall architectures. [ref]
Basic local alignment search tool by Stephen F. Altschul and others. 1990, word hits, extension and local similarity search
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