[Biopython] How to get intron/exon boundaries?

[Sean Davis]

On Sun, Nov 29, 2009 at 10:30 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> 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.

http://genome.ucsc.edu/cgi-bin/hgTables?org=Mouse

Choose the track that you like.  UCSC Known Genes is the typical default.

There are numerous output format options.  Again, choose whatever you
think is convenient.  The outputs are almost all tab-delimited text,
so you should be able to use them easily in the scripting language of
your choice.  If you prefer gff, then consider GTF format.

If you have questions for the UCSC folks, they have their own mailing
list accessible from the top of the page on their website.

Sean


>>>> 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
>>
>
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