sorry, can you clarify: what do you mean with you "get mostly -ve" ?
Andreas On Fri, Mar 19, 2010 at 3:50 AM, Shakuntala baichoo <[email protected]>wrote: > 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
