[BiO BB] how to find gene neighbours

[Pankaj]

Hi Pooja,
Nops!
By gene neighbours I mean genes which are positionally close together on the
genome, ie adjoining genes.
Although I found the NCBI's map viewer friendly, but I couldnt figure out how
 to automate a script which can find gene neighbours for all the GI's that I
have. Presently, having a GI number I can find gene neighbours manually by
looking at the chromosome map, but I dont know how data is organised in the
database, so that I can automate the process.
Any help on this will be highly appreciated!
Cheers,
Pankaj Khurana

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Open WebMail Project (http://openwebmail.org)


---------- Original Message -----------
From: Pooja Jain <pjain at xldb.di.fc.ul.pt>
To: pankaj at nii.res.in
Sent: Tue,  7 Feb 2006 17:51:17 +0000
Subject: Re: [BiO BB] how to find gene neighbours

> Hi,
> Probably u will be interested in idetifying the set of GI numbers 
> from the GI number you have which share evolutionaly relationship. 
> In other words you are trying to find genes from different organisms 
> which are neighbours during their parallel evolution. Am I 
> understood you correctly ?
> 
> cheers!
> 
> -Pooja
> Citando Pankaj <pankaj at nii.res.in>:
> 
> >
> > Thankx Govind!
> >
> > I have gi numbers of homologous proteins from different organisms (some of
> > which may be sequenced and some may not be....i dont know!). I want to know
> > how to find gene neighbours and then automate the script to find gene
> > neighbours for all the gi numbers that I have.
> >
> > Pankaj Khurana
> >
> > --
> > Open WebMail Project (http://openwebmail.org)
> >
> >
> > ---------- Original Message -----------
> > From: govind mk <mkgovindis at yahoo.com>
> > To: idoerg at burnham.org, "The general forum at Bioinformatics.Org"
> > <bio_bulletin_board at bioinformatics.org>
> > Sent: Wed, 1 Feb 2006 18:46:31 -0800 (PST)
> > Subject: Re: [BiO BB] how to find gene neighbours
> >
> > > I think NCBI's map viewer can elp you find neighbouring genes
> > > .....   Are u looking for an algorithm or just want to map you genes
> > > on to genomes and identify their neighbours
> > >
> > >   -Govind
> > >
> > >
> > > Iddo Friedberg <idoerg at gmail.com> wrote:
> > >   Generally, you can do that by going to the genomic database of
> > > choice for your particular organism. As you have not mentioned which
> > > organism those genes are form, it is rather hard to make a
> > > recommendation. Ensembl, www.fruitfly.org, yeastgenome.org are
> > > examples of such databases for Eukaryotic models.
> > >
> > > A list for bacterial projects is available from :
> > >
> > >
> > http://www.pasteur.fr/recherche/unites/tcruzi/minoprio/genomics/bacteria.htm
> > >
> > > HTH,
> > >
> > > Iddo
> > >
> > > Pankaj wrote:
> > >
> > > >Hi Everybody,
> > > >I have a few gi numbers. I want to find the their neighbouring genes. How
> > can
> > > >I do that?
> > > >
> > > >Thanking all in advance
> > > >
> > > >Pankaj Khurana
> > > >
> > > >
> > > >--
> > > >Open WebMail Project (http://openwebmail.org)
> > > >
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> > > >
> > > >
> > > >
> > > >
> > >
> > > --
> > > Iddo Friedberg, Ph.D.
> > > Burnham Institute for Medical Reseach
> > > 10901 N. Torrey Pines Rd.
> > > La Jolla, CA 92037 USA
> > > Tel: +1 (858) 646 3100 x3516
> > > Fax: +1 (858) 713 9949
> > > http://iddo-friedberg.org
> > > http://BioFunctionPrediction.org
> > >
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------- End of Original Message -------