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

[Andreas Prlic]

Hi Shakuntala,

at the present the NeedlemanWunch implementation does not make it totally
straightforward to access the %id. You could try parsing the result of the
getAlignmentString() call and accessing the information from there ...
Making the underlying data more accessible is on the TODO list for this
module: http://biojava.org/wiki/BioJava:Modules

Andreas

2010/3/21 Shakuntala baichoo <shakunb at uom.ac.mu>

> Hi Andreas!
> The problem is as follows. We have a bacteria file. There are about 565
> named genes/features there. We wish to compare each gene with the other 564
> genes. I am using needleman-wunsch from biojava to do so. For one specific
> run, I am attaching the result.
> The score after comparing Feature no. 0 with Feature no. 1 to Feature no.
> 564 is displayed (along with the product name etc...). If I wish to
> interpret these scores as a percentage homology, how do I do it?
>
> P.S. Most of the scores are -ve. Only one or a few is +ve.  The comparison
> is done using NUCC44.txt.
>
> Thanks
> Kind Regards
> Shakuntala
>
>
> On Fri, Mar 19, 2010 at 9:42 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> 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:
>>>
>>> > Send Biojava-l mailing list submissions to
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>>> >
>>> > 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 <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
>>> > >
>>> >
>>> >
>>> > ------------------------------
>>> >
>>> > _______________________________________________
>>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> > 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  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>>
>
>
> --
> Best Regards
>
> Dr. (Mrs.) S.Baichoo
> Senior Lecturer
> CSE Dept, FoE
> University of Mauritius
>