Acceleration of tag placement using custom hardware
AssigneePioneer Hi-Bred International, Inc.
InventorKent Allan Vander Velden
Life of this patent
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Abstract
A hardware device is configured to accelerate the process of determining the location of a query sequence (a tag) within a sequence library (such as a reference genome) using one or more comparison units having inputs for receiving the query sequence and a subsequence of the sequence library (a k-mer) and an output for reporting results where each comparison unit is capable of searching the tag in the sense and the antisense orientation against the sequence library in the sense and antisense orientation. Methods and systems are also provided.
Claims24
An apparatus for locating a query sequence in a sequence library, the apparatus comprising:
- a plurality of comparison units operatively connected in parallel wherein each of the plurality of comparison units are configured for comparing (a) the query sequence in the sense orientation and the sequence library in the sense orientation, (b) the query sequence in the antisense orientation and the sequence library in the sense orientation, (c) the query sequence in the sense orientation and the sequence library in the antisense orientation, and (d) the query sequence in the antisense orientation and the sequence library in the antisense orientation;
- each of the plurality of comparison units having an input for receiving the query sequence;
- each of the plurality of comparison units having an input for receiving a subsequence of the sequence library;
- and
- each of the plurality of comparison units having an output for reporting results.
A method for locating a query sequence in a sequence library, the method comprising:
- providing a hardware device comprising a plurality of comparison units configured to locate the query sequence within the sequence library;
- providing at least one query to the hardware device;
- providing a plurality of subsequences of the sequence library to the hardware device;
- and
- receiving results from the hardware device indicative of the location of the query sequence within the provided subsequences of the sequence library.
Dependencies are inferred from the claim text.