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

[Shakuntala baichoo]

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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>   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