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  • ferdinand_marletaz
    Hello, I m currently writing a program to play with Traces and I would like to use SSAHA2 in it. But I would like to would if it is possible to create prebuild
    Message 1 of 2 , Sep 7, 2006
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      Hello,

      I'm currently writing a program to play with Traces and I would like
      to use SSAHA2 in it.
      But I would like to would if it is possible to create prebuild hash
      for very large subject like a whole trace archive. Must I use
      SSAHA2server even if I'm computing only on a single machine ? Is it
      possible to use such prebuild hashes with a direct fasta input just
      like in SSAHA2 ?

      Thank you very much for your advices

      Ferdi



      °°°°°°°
      Ferdinand Marlétaz
      Phylogeny and evolution of Metazoans
      Station Marine d'Endoume
      Marseille, France
      ferdinand.marletaz@...
    • Adam Spargo
      Hi, This isn t implemented properly in ssaha2 yet. (The standalone version uses a slightly different format for the hash which isn t nice for saving. I will
      Message 2 of 2 , Sep 7, 2006
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        Hi,
        This isn't implemented properly in ssaha2 yet. (The standalone version
        uses a slightly different format for the hash which isn't nice for saving.
        I will convert it to use the same format as the server sometime, but have
        more urgent things to do).

        You should use the server for the present. This is probably a good idea
        anyway if you want to search a large archive. Even if you have the hash
        saved you still have to read it into memory which can take a couple of
        minutes - you don't want to do that for every search. Better to leave the
        server running.

        We have a distributed version of ssaha2 which we use to search the trace
        archive at Sanger:

        http://trace.ensembl.org/cgi-bin/tracesearch

        But this is more problematic to install and so is not available for
        download yet. If you find that your hashtable is too big for a single
        machine, get back to me and we can talk about installing the distributed
        system at your site.

        Cheers,

        Adam.

        --
        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, 7 Sep 2006, ferdinand_marletaz wrote:

        > Hello,
        >
        > I'm currently writing a program to play with Traces and I would like
        > to use SSAHA2 in it.
        > But I would like to would if it is possible to create prebuild hash
        > for very large subject like a whole trace archive. Must I use
        > SSAHA2server even if I'm computing only on a single machine ? Is it
        > possible to use such prebuild hashes with a direct fasta input just
        > like in SSAHA2 ?
        >
        > Thank you very much for your advices
        >
        > Ferdi
        >
        >
        >
        > °°°°°°°
        > Ferdinand Marlétaz
        > Phylogeny and evolution of Metazoans
        > Station Marine d'Endoume
        > Marseille, France
        > ferdinand.marletaz@...
        >
        >
        >
        >
        >
        >
        >
        >
        > Yahoo! Groups Links
        >
        >
        >
        >
        >
        >
        >
        >
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