Announcement: Version 2.0 of SSAHA

[Tony Cox]

We are pleased to announce an improved version of our SSAHA software for 
very fast matching and alignment of DNA and protein sequence data.
It is capable of searching human-genome sized databases at a speed that is
around 3 orders of magnitude faster than BLAST.

You may use SSAHA to search against the latest human `golden path' 
assembly (3.2 gigabases):
http://www.ensembl.org/perl/ssahaview

You may use SSAHA to search against the Ensembl Trace Repository
(currently over 23 million traces, 11 gigabases):
http://trace.ensembl.org/perl/ssahaview

SSAHA is available for download (as a tool which runs from the UNIX
command line) from:
http://www.sanger.ac.uk/Software/analysis/SSAHA/

New features for this version:

As well as DNA against DNA matching it can now also search ... 

 - protein query against protein database
 - DNA query against protein database (i.e. do 6-way translation then
   search)
 - protein query against 6-way translated DNA database (i.e. look for DNA
   that codes for your protein) 
 - 6-way translated DNA query against 6-way translated DNA database

Improved matching: now gives percentage identity for each match, plus better
handling of gaps, indels and tandem repeats.

Better output: choice of output formats, can produce sorted lists of matches. 

Tony Cox

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  Dr. Anthony J. Cox              -.   .-. .-.   .-. .-.   .-
  Team 71, Informatics Division,  ||\ /|||X|||\ /|||X|||\ /||   
  The Sanger Centre,              |||X|||/ \|||X|||/ \|||X|||
  Hinxton, Cambridge CB10 1SD, UK `-' `-'   `-' `-'   `-' `-'
   -.   .-. .-.   .-. .-.   .-
   ||\ /|||X|||\ /|||X|||\ /||         ac2 at sanger.ac.uk
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