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Indexing a reference sequence for oligomer sequence mapping

  • US 8,738,296 B2
  • Filed: 02/02/2010
  • Issued: 05/27/2014
  • Est. Priority Date: 02/03/2009
  • Status: Active Grant
First Claim
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1. A method of generating an index, the index operable to determine where, in a reference sequence, a data set of one or more related oligomer sequences maps to the reference sequence, the oligomer sequences of the data set obtained from a same fragment of genetic material, the method comprising:

  • applying, with a computer system, a key pattern to the reference sequence to generate a plurality of keys, wherein the key pattern includes a first set of N contiguous positions separated by K positions from a second set of M contiguous positions, the separation being based on predicted relationships between oligomer sequences of the data set, wherein the key pattern is defined by predetermined values for N, K and M, the applying including;

    applying the key pattern to a first location of the reference sequence to obtain a first set of bases, the first set of bases including;

    N contiguous bases of the reference sequence starting from the first location, andM contiguous bases of the reference sequence starting from N+K positions after the first location, N, M, and K being integers greater than or equal to one;

    using the first set of bases to generate a first key;

    applying the key pattern to a plurality of other locations to generate other keys, wherein the applying of the key pattern to the first and other locations uses the same values for N, M, and K; and

    storing the keys in the index, the index being stored in a searchable computer readable medium;

    wherein each key corresponds to one or more possible locations within the reference sequence.

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