[Biopython] How to get intron/exon boundaries?

[Peng Yu]

On Sun, Nov 29, 2009 at 6:55 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Fri, Nov 27, 2009 at 7:18 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>> On Fri, Nov 27, 2009 at 5:03 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>>> On Fri, Nov 27, 2009 at 10:56 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>>>> I'm wondering how to get intron exon boundaires for all the genes.
>>>> Could somebody show me what functions I should use?
>>>
>>> What do you want to know? The co-ordinates of the intron/exons,
>>> or just to get the coding sequence?
>>
>> I want the co-ordinates.
>
> You are talking about coordinates in genomic space or on the
> transcript?  What organism?  And what annotation system do you want to
> use--Ensembl, UCSC, or NCBI?

The coordinates in genomic space. Mouse. UCSC.

>>> What kind of data are you looking at? For GenBank or EMBL
>>> files this is encoded in the CDS feature locations. For GFF
>>> files I think this information is given explicitly,
>>
>> Would you please let me know how to get the CDS feature locations from
>> GenBank and EMBL? What are GFF files?
>
> For GFF, google will get you a long way ("GFF format").
>
> Sean
>