Method and Apparatus for Performing Similarity Searching
First Claim
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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Accused Products
Abstract
A system and method for performing similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching 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 pipeline may further include an ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.
169 Citations
68 Claims
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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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34)
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35. A method for performing similarity searching, the method comprising:
processing a data stream with a programmable logic device configured to include a pipeline that comprises a matching stage and a downstream ungapped extension prefilter stage, wherein the processing step comprises; the matching stage receiving the data stream, the data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string; and the ungapped extension prefilter stage shifting through pattern matches between the data strings and the plurality of substrings of the query string and providing a score so that only pattern matches that exceed a user defined score will pass downstream from the ungapped extension prefilter stage. - View Dependent Claims (36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68)
Specification