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Re: [ssahausers] Screen Traces

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  • 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 1 of 2 , Sep 7, 2006
      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@...
      >
      >
      >
      >
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