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Method and Apparatus for Performing Similarity Searching

  • US 20110231446A1
  • Filed: 03/11/2011
  • Published: 09/22/2011
  • Est. Priority Date: 03/03/2005
  • Status: Active Grant
First Claim
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1. A digital logic circuit for performing biological sequence similarity searching, the circuit comprising:

  • a programmable logic device configured to include a pipeline that comprises a matching stage and a downstream ungapped extension prefilter stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string, the ungapped extension prefilter stage being configured to (1) shift through pattern matches between the data strings and the plurality of substrings of a query string and (2) provide a score so that only pattern matches that exceed a user defined score will pass downstream from the ungapped extension prefilter stage.

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