![]() When we say that sequence A has high homology to sequence B, then we are making two distinct claims: not only are we saying that sequences A and B look much the same, but also that all of their ancestors also looked the same, going all the way back to a common ancestor. The term 'sequence homology' is the most important (and the most abused) of the three. Sequence similarity takes approximate matches into account, and is meaningful only when such substitutions are scored according to some measure of 'difference' or 'sameness' with conservative or highly probably substitutions assigned more favorable scores than non-conservative or unlikely ones. Sequence identity refers to the occurrence of exactly the same nucleotide or amino acid in the same position in aligned sequences. Even though they are often used interchangeably, they have quite different meanings. In describing sequence comparisons, several different terms are commonly (mis)used: identity, similarity and homology. Further details can be found in several excellent resources, and additional BLAST-based programs are listed in Table 1. This article discusses the principles, workings, applications and potential pitfalls of BLAST, focusing on the NCBI version. NCBI BLAST is available from the National Center for Biotechnology Information (NCBI), while WU-BLAST is available from Washington University in St. Today there are several implementations of the BLAST algorithm, with two that share a common ancestry - NCBI BLAST and WU-BLAST - enjoying the broadest use. It is therefore important to know how it works and what it accomplishes, how to use it properly and how to interpret someone else's published results (see Box 1). In the 11 years since its publication, the original paper describing BLAST has been cited over 12,000 times, and use of BLAST has become a fundamental tool of biology. The most popular tool for this purpose is BLAST (basic local alignment search tool), which performs comparisons between pairs of sequences, searching for regions of local similarity. Similarity searching, including sequence comparison, is one of the principal techniques used by computational biologists and has found widespread use among biologists in general.
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