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

[Sean Davis]

On Thu, Feb 14, 2008 at 1:02 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

UCSC and Ensembl both offer simple tools for doing this sort of thing.
 In UCSC, they call it the "table browser", while in Ensembl, they
call it ensmart.  Both allow you to specify a region and get various
interesting pieces of information from those regions.  I would look at
those two interfaces, as they will do what you need.  Alternatively,
both offer open MySQL access to the underlying databases.  Of course,
this assumes that the organism that you are interested in is available
in UCSC and/or Ensembl.  If you need more details, feel free to
ask....

Sean