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
Phylogeny and evolution of Metazoans
Station Marine d'Endoume
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
We have a distributed version of ssaha2 which we use to search the trace
archive at Sanger:
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.
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:
> 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
> Ferdinand Marlétaz
> Phylogeny and evolution of Metazoans
> Station Marine d'Endoume
> Marseille, France
> Yahoo! Groups Links