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 <[email protected]>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 <[email protected]> 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 <[email protected]> >> >> 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 <[email protected]> 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 >>>> <[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 >>>>> >>>> >>>> >>> >>> >>> -- >>> 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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
