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Method and Apparatus for Protein Sequence Alignment Using FPGA Devices

  • US 20080086274A1
  • Filed: 08/10/2007
  • Published: 04/10/2008
  • Est. Priority Date: 08/10/2006
  • Status: Abandoned Application
First Claim
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1. A data processing apparatus for sequence alignment searching, the apparatus comprising:

  • a first stage configured to (1) receive a bit stream that is representative of a database sequence and (2) process the bit stream to produce a plurality of seeds, each seed being indicative of a similarity between a substring of the database sequence and a substring of a query sequence;

    a second stage configured to perform an ungapped extension analysis on the seeds generated by the first stage, thereby generating a plurality of high scoring pairs (HSPs); and

    a third stage configured to perform a gapped extension analysis on the HSPs generated by the second stage, thereby determining whether any HSPs exist that will produce alignment of interest between the database sequence and the query sequence; and

    wherein the first stage, the second stage, and at least a portion of the third stage are implemented as a data processing pipeline on at least one hardware logic device.

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