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Group Information

  • Members: 46
  • Category: Genetics
  • Founded: May 28, 2002
  • Language: English
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Description

This group is for help and discussion concerning the SSAHA
software package for rapid searching of DNA and protein
databases.

The latest version of this software may be downloaded for free
by joining this group (your email address will not be shared or
misused in any way). The software is released under the GNU GPL.

This package was produced at the Wellcome Trust Sanger Institute,
however the version available from their website is somewhat out
of date.
http://www.sanger.ac.uk/Software/analysis/SSAHA/

The Sanger Institute have also produced a package SSAHA2, please
note SSAHA2 requires a license for the Phrap/cross-match package
it makes use of, hence is not free for non-academic users.
http://www.sanger.ac.uk/Software/analysis/SSAHA2/

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Re: SSAHA2 setup to search for primer binding sites
Hi Adam, Thanks for the quick response. Do you have any idea of the amount of memory neccessary to build the hashtable of the Human genomic sequence? I am
Posted - Wed Oct 17, 2007 2:00 pm
 edburke1979
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Re: SSAHA2 setup to search for primer binding sites
Hi, To hit short reads allowing mis-matches you will need to use -skip 1, kmer 12 is usually fine. Cheers. -- Dr Adam Spargo High Performance Assembly Group
Posted - Fri Oct 12, 2007 1:27 pm
 Adam Spargo
a_w_spargo
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SSAHA2 setup to search for primer binding sites
Hi, I am trying to setup SSAHA2 to search for primer binding sites in the human genome. The app we currently have that does this uses BLAST, but I would like
Posted - Thu Oct 11, 2007 11:08 am
 edburke1979
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Re: Error running latest ssaha
... Having looked at this some more I found that if you use a full path to specify the location of the fasta file when you create the hash initially you can
Posted - Fri Aug 24, 2007 10:16 am
 sraxylan
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Re: Error running latest ssaha
You're right, there does seem to be an issue when you specify '-sf hash' - both query and subject need to be in the same directory. Interestingly it always
Posted - Thu Aug 23, 2007 2:19 pm
 coxtonyj
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2007 8 1 1 5 5 3
2006 6 3 4 10 1 1 4 2
2005 3 1 2 2
2004 1
2003 2 3 12 2 2
2002 6 8 3 5
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