METHOD AND APPARATUS FOR PERFORMING BIOSEQUENCE SIMILARITY SEARCHING

摘要

An apparatus and method for performing similarity searching on a data stream with respect to a query string are disclosed, where the data stream comprises a plurality of data substrings, and where the query string comprises a plurality of query substrings. A programmable logic device is used to filter the data stream to find a plurality of possible matches between the data substrings and a plurality of the query substrings, wherein the data substrings and the query substrings comprise a plurality of characters. From these possible matches, a determination can be made as to a similarity between the query string and at least a portion of the data stream.