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106Re: SSAHA2 setup to search for primer binding sites

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  • edburke1979
    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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