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104SSAHA2 setup to search for primer binding sites

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  • edburke1979
    Oct 11, 2007
      Hi,

      I am trying to setup SSAHA2 to search for primer binding sites in the
      human genome. The app we currently have that does this uses BLAST, but
      I would like to speed up the search.

      The primers will be 15-30bp and I want to allow for up to 2 mismatches
      between query and target.

      I am planning to read the hashtable in from disk rather store in memory.

      Can anyone suggest some appropriate values for -skip and -kmer for
      ssaha2Build?

      Best Regards,

      Ed
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