Hi! I would like to know the interpretation of the scores after running the needleman-wunsch algorithm using the NUCC44.txt substitution matrix. Actually I have taken the named genes from a bacteria EMBL file and I am trying to compare each gene to the other genes in the lot, using the needleman-wunsch algorithm based on the NUCC44.txt substitution matrix. I would like to determine the % match for each pair but since I get mostly -ve and some positive values, I would like to know how to calculate the % match for a pair of genes. I would be grateful if anybody could help me.
Thanks. Shakuntala On Thu, Mar 18, 2010 at 8:00 PM, <[email protected]>wrote: > Send Biojava-l mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > > Today's Topics: > > 1. Re: SVN repository (Andreas Prlic) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 17 Mar 2010 10:39:41 -0700 > From: Andreas Prlic <[email protected]> > Subject: Re: [Biojava-l] SVN repository > To: Richard Finkers <[email protected]> > Cc: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > I have just heard back from the OBF-helpdesk. The VM hosting the anonymous > SVN is currently down. Depending on how big the problem turns out to be, it > will be back at some point later today / should be back latest tomorrow. > > Sorry for this inconvenience. > Andreas > > > > > On Wed, Mar 17, 2010 at 3:16 AM, Peter <[email protected] > >wrote: > > > On Wed, Mar 17, 2010 at 7:21 AM, Richard Finkers <[email protected] > > > > wrote: > > > > > > Hi, > > > > > > I would like to have a look at the BioJava 3 code (and perhaps in the > > future > > > contribute to). However, I cannot access the SVN repository > > > ( > > > http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk > > ). > > > > > > Is the repository down? > > > > > > Thanks, > > > Richard > > > > Probably :( > > > > There have been problems discussed on the BioPerl mailing list > > (they use the same servers), and the OBF team are aware of it: > > http://lists.open-bio.org/pipermail/bioperl-l/2010-March/032534.html > > > > The code.open-bio.org repositories are a read only public mirror, > > while dev.open-bio.org is the master repository I think is fine > > (but not available for anonymous download). > > > > In the mean time BioPerl have also setup a read only mirror > > on github - perhaps BioJava could do the same? Meanwhile > > BioRuby and Biopython are just using github (not SVN or CVS). > > > > Peter > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > End of Biojava-l Digest, Vol 86, Issue 9 > **************************************** > -- Best Regards Dr. (Mrs.) S.Baichoo Senior Lecturer CSE Dept, FoE University of Mauritius _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
