[Biojava-l] Biojava-l Digest, Vol 86, Issue 9

[Andreas Prlic]

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 <shakunb at uom.ac.mu>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, <biojava-l-request at lists.open-bio.org
> >wrote:
>
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> > Today's Topics:
> >
> >   1. Re: SVN repository (Andreas Prlic)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 17 Mar 2010 10:39:41 -0700
> > From: Andreas Prlic <andreas at sdsc.edu>
> > Subject: Re: [Biojava-l] SVN repository
> > To: Richard Finkers <Richard.Finkers at wur.nl>
> > Cc: biojava-l at lists.open-bio.org
> > Message-ID:
> >        <59a41c431003171039h4ca1267bibc45b0d7d270b2a9 at mail.gmail.com>
> > 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 <biopython at maubp.freeserve.co.uk
> > >wrote:
> >
> > > On Wed, Mar 17, 2010 at 7:21 AM, Richard Finkers <
> Richard.Finkers at wur.nl
> > >
> > > 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  -  Biojava-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > >
> >
> >
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> >
> > End of Biojava-l Digest, Vol 86, Issue 9
> > ****************************************
> >
>
>
>
> --
> Best Regards
>
> Dr. (Mrs.) S.Baichoo
> Senior Lecturer
> CSE Dept, FoE
> University of Mauritius
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