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

Wed Mar 24 15:37:43 UTC 2010

Hi Shakuntala,

If the score is positive or negative only depends on the implementation and
representation... I think most people expect the score to be positive, so
the toAlignmentString method displays it as a positive value, while
internally it is a bit different...

Andreas

On Wed, Mar 24, 2010 at 3:32 AM, Shakuntala baichoo <shakunb at uom.ac.mu>wrote:

> Hello Andreas!
> Thanks for the quick reply.
> I tried the getAlignmentString. It provides a lot of information. However,
> I think there is a slight problem here. From the getAlignmentString call I
> see that the score after aligning a pair of dna strings is 2706.
> But when I view the return value from the method pairwiseAlignment (for the
> same set) then the score is -2706.  Why?
>
> Thanks
> Shakuntala
>
> *
> *
>
>
> On Tue, Mar 23, 2010 at 3:46 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> 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
>>>>> >        biojava-l at lists.open-bio.org
>>>>> >
>>>>> > 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
>>>>> >        biojava-l-request at lists.open-bio.org
>>>>> >
>>>>> > You can reach the person managing the list at
>>>>> >        biojava-l-owner at lists.open-bio.org
>>>>> >
>>>>> > 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
>>>
>>
>>
>
>
> --
> Best Regards
>
> Dr. (Mrs.) S.Baichoo
> Senior Lecturer
> CSE Dept, FoE
> University of Mauritius
>