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 -. .-. .-. .-. .-. .-
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