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SSAHA2 setup to search for primer binding sites

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  • edburke1979
    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
    Message 1 of 3 , Oct 11, 2007
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      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
    • Adam Spargo
      Hi, To hit short reads allowing mis-matches you will need to use -skip 1, kmer 12 is usually fine. Cheers. -- Dr Adam Spargo High Performance Assembly Group
      Message 2 of 3 , Oct 12, 2007
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        Hi,
        To hit short reads allowing mis-matches you will need to use -skip 1, kmer
        12 is usually fine.

        Cheers.

        --
        Dr Adam Spargo
        High Performance Assembly Group email: aws@...
        Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
        Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919

        On Thu, 11 Oct 2007, edburke1979 wrote:

        > 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
        >
        >
        >
        >
        > Yahoo! Groups Links
        >
        >
        >
        >


        --
        The Wellcome Trust Sanger Institute is operated by Genome Research
        Limited, a charity registered in England with number 1021457 and a
        company registered in England with number 2742969, whose registered
        office is 215 Euston Road, London, NW1 2BE.
      • edburke1979
        Hi Adam, Thanks for the quick response. Do you have any idea of the amount of memory neccessary to build the hashtable of the Human genomic sequence? I am
        Message 3 of 3 , Oct 17, 2007
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          Hi Adam,

          Thanks for the quick response.

          Do you have any idea of the amount of memory neccessary to build the
          hashtable of the Human genomic sequence? I am running out of memory
          when trying to use skip of 1 and kmer of 12. We only have 1GB free on
          the server at the moment.

          Best Regards,

          Ed

          --- In ssahausers@yahoogroups.com, Adam Spargo <aws@...> wrote:
          >
          > Hi,
          > To hit short reads allowing mis-matches you will need to use -skip
          1, kmer
          > 12 is usually fine.
          >
          > Cheers.
          >
          > --
          > Dr Adam Spargo
          > High Performance Assembly Group email: aws@...
          > Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
          > Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919
          >
          > On Thu, 11 Oct 2007, edburke1979 wrote:
          >
          > > 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
          > >
          > >
          > >
          > >
          > > Yahoo! Groups Links
          > >
          > >
          > >
          > >
          >
          >
          > --
          > The Wellcome Trust Sanger Institute is operated by Genome Research
          > Limited, a charity registered in England with number 1021457 and a
          > company registered in England with number 2742969, whose registered
          > office is 215 Euston Road, London, NW1 2BE.
          >
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