Announcement: Version 2.0 of SSAHA

Tony Cox ac2 at sanger.ac.uk
Fri Jul 20 03:11:50 EST 2001


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
   |||X|||/ \|||X|||/ \|||X|||            
   `-' `-'   `-' `-'   `-' `-'
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