[Bioperl-l] [Genome] TraceSearch

Jim Kent kent at soe.ucsc.edu
Fri Mar 31 01:09:19 EST 2006


Very nice.   It takes a very long time to search the NCBI trace  
archives.
I've been tinkering a little on a tool that might let you do more  
sensitive
searches in reasonable time, but it would require a LOT of RAM for
the trace archives!   How much RAM are you using for your SSAHA
servers?

On Mar 30, 2006, at 4:43 AM, Adam Spargo wrote:

> Hi,
> We would like to announce the launch of a new free service which gives
> public access to the Wellcome Trust Sanger Institute Trace Archive via
> sequence similarity. The archive contains records of all publicly
> available DNA sequencing reads. The search engine, available at:
>
> http://trace.ensembl.org/cgi-bin/tracesearch
>
> allows users to identify any sequences in the archive with significant
> similarity to their query sequence. Users are able to search the whole
> archive in a few seconds, or alternatively to limit the search by  
> species,
> sequencing centre or trace type. We use a version of the SSAHA  
> algorithm
> to distribute an index over a cluster of machines so that we can  
> continue
> to scale the service as the archive grows.
>
> Full Story:
>
> http://www.sanger.ac.uk/Info/Press/
>
> We welcome any feedback and suggestions for improvements to this  
> service.
>
> Please forward this email to collegues and collaborators who may be
> interested.
>
> Thanks,
>
> On behave of the TraceSearch development team.
>
> -- 
> Dr Adam Spargo
> High Performance Assembly Group   email: aws at sanger.ac.uk
> Wellcome Trust Sanger Institute   Tel: +44 (0)1223 834244 x7728
> Hinxton, Cambridge CB10 1SA       Fax: +44 (0)1223 494919
>
>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome



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