http://groups.yahoo.com/group/ssahausers/ SSAHA Users Wed, 17 Oct 2007 14:00:17 GMT edburke1979 http://groups.yahoo.com/group/ssahausers/message/106 http://groups.yahoo.com/group/ssahausers/message/106 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 Fri, 12 Oct 2007 13:27:03 GMT Adam Spargo http://groups.yahoo.com/group/ssahausers/message/105 http://groups.yahoo.com/group/ssahausers/message/105 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 Thu, 11 Oct 2007 11:08:46 GMT edburke1979 http://groups.yahoo.com/group/ssahausers/message/104 http://groups.yahoo.com/group/ssahausers/message/104 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 Fri, 24 Aug 2007 10:16:19 GMT sraxylan http://groups.yahoo.com/group/ssahausers/message/103 http://groups.yahoo.com/group/ssahausers/message/103 ... 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 Thu, 23 Aug 2007 14:19:55 GMT coxtonyj http://groups.yahoo.com/group/ssahausers/message/102 http://groups.yahoo.com/group/ssahausers/message/102 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 Thu, 23 Aug 2007 13:03:55 GMT sraxylan http://groups.yahoo.com/group/ssahausers/message/101 http://groups.yahoo.com/group/ssahausers/message/101 ... Tony, Thanks for the reply. I've checked, and test.fa is definitely using unix line endings already. Having played with this a bit more it seems this is Thu, 23 Aug 2007 11:31:38 GMT coxtonyj http://groups.yahoo.com/group/ssahausers/message/100 http://groups.yahoo.com/group/ssahausers/message/100 Hi Your command should work if test.fa is in valid fasta format. However the file needs to be in UNIX text file format - ie just one character at each Thu, 23 Aug 2007 08:29:40 GMT sraxylan http://groups.yahoo.com/group/ssahausers/message/99 http://groups.yahoo.com/group/ssahausers/message/99 I'm trying to run ssaha on a fedora 7 (32bit) system and it's dying with an error every time I run it. I'm running the latest v33 version of ssaha, but I've Sun, 20 May 2007 01:42:23 GMT Charles Plessy http://groups.yahoo.com/group/ssahausers/message/98 http://groups.yahoo.com/group/ssahausers/message/98 ... Dear Tony, many thanks! I will announce on this mailing list when the Debian package will be ready. Have a nice day, -- Charles Plessy Fri, 18 May 2007 10:32:57 GMT coxtonyj http://groups.yahoo.com/group/ssahausers/message/97 http://groups.yahoo.com/group/ssahausers/message/97 Dear Charles/Adam I have made the changes necessary to get 'original' SSAHA to compile under gcc 4.1.2 and uploaded a new version of the package to this group Fri, 18 May 2007 10:16:23 GMT http://groups.yahoo.com/group/ssahausers/message/96 http://groups.yahoo.com/group/ssahausers/message/96 Hello, This email message is a notification to let you know that a file has been uploaded to the Files area of the ssahausers group. File : Sat, 05 May 2007 09:09:55 GMT Charles Plessy http://groups.yahoo.com/group/ssahausers/message/95 http://groups.yahoo.com/group/ssahausers/message/95 ... Dear Adam, there is a major difference between SSAHA and SSAHA2: the first is free software, and unfortunately the second is not. I would be happy to Fri, 04 May 2007 15:30:26 GMT Adam Spargo http://groups.yahoo.com/group/ssahausers/message/94 http://groups.yahoo.com/group/ssahausers/message/94 Hi, Sorry if I haven't replied to resent requests in person, all reported issues should be solved by this new release: Mon, 09 Apr 2007 21:01:52 GMT erika-haven347@... http://groups.yahoo.com/group/ssahausers/message/93 http://groups.yahoo.com/group/ssahausers/message/93 oh yeah man i didnt believe how good it was http://www.bestsoftwaresforyou.biz/ohgf Fri, 30 Mar 2007 07:18:34 GMT dorie-chabot819@... http://groups.yahoo.com/group/ssahausers/message/92 http://groups.yahoo.com/group/ssahausers/message/92 download new games movies software http://www.cs2-softwares.info/cpto