Abstract
Of the many problems in biological data retrieval, the problem of biological sequence retrieval has the highest profile. The standard solution to this problem, BLAST, has ascended, like google , to become synonymous with search. Also like Google, BLAST leverages statistical properties as heuristics to create a good user experience. Ironically, many early biological sequence similarity efforts explicitly sought to model evolutionary distance as a metric-distance. Recent interest in metric-index methods has rekindled these early directions. A review of these efforts provides an opportunity to characterize the challenges and opportunities in similarity search of biological data.
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