[Biopython] How to get sequences upstream of TSS of genes?

[Steve Lianoglou]

Hi,

On Oct 16, 2009, at 10:52 AM, Peng Yu wrote:

> On Fri, Oct 16, 2009 at 3:29 AM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
>> On Thu, Oct 15, 2009 at 11:17 PM, Peng Yu <pengyu.ut at gmail.com>  
>> wrote:
>>> I have a set of genes. I want to get the 5kb sequence that is  
>>> upstream
>>> of the TSS's of each gene.
>>
>> You can do that with biomart:
>> - http://www.ensembl.org/biomart/martview/a90f00892a48e04d438f762f551bf48a/a90f00892a48e04d438f762f551bf48a
>>
>> select Ensembl56 as database, Mus Musculus as species, go to Filters
>> and fill the 'Id list limit' form to add the required geneIds, then  
>> go
>> to Attributes, select Sequences and then check 'Upstream Flank -
>> 5000'.
>
> I have gene names (for example, Krt83) what geneIDs shall I choose?

Since your on ensembl's web site, I'd imagine ensembl gene id's might  
be a good bet, no? :-)

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact