[BioPython] retrieve sequence coordinates of exons for a stretch of genes

[Peter Cock]

Hi Kevin,

Where do you normally get your genomes from? I am most familiar with
the NCBI formats, so I would start by examining the GenBank file for
the relevant genome.  Have a look by hand first - it may well have
features for these genes, and in particular a CDS feature which marks
out the introns/exons for you.

Biopython will read GenBank files, although I would say dealing with
the locations via the SeqFeature object is a little fiddly... have a
look at the main documentation and also perhaps
http://www2.warwick.ac.uk/go/peter_cock/python/genbank/

Peter

On Thu, Feb 14, 2008 at 6:02 AM, Kevin Lam <ULNJUJERYDIX at spammotel.com> wrote:
> Hi
>  I have been scouring through the web for something I thought was a rather
>  simple task but I can't find the answer.
>
>  How do I get the sequence coordinates for exons of genes in a stretch of
>  genome demarcated by say HoxA13 and Hox A1 ?
>
>  below is the example of the data I am looking for.
>
>  1026087..1026688    1026807..1026834    1026839..1027045    HOXD12
>  1033641..1034421    1035192..1035427    1035428..1035873    HOXD11
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