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

[Giovanni Marco Dall'Olio]

On Fri, Oct 16, 2009 at 5:44 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
> On Fri, Oct 16, 2009 at 10:24 AM, Giovanni Marco Dall'Olio
> <dalloliogm at gmail.com> wrote:
>> On Fri, Oct 16, 2009 at 4:55 PM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com> wrote:
>>> 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:
>>>>>
>>>>
>>>> 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? :-)
>>
>> exactly, but if you look at the form more carefully you will see that
>> there is a menu from which you can choose the type of geneId, for
>> example: ensembl, kegg, ncbi, etc...
>>
>> note: I didn't send you the ufficial biomart's link. The right one is:
>> - http://www.ensembl.org/biomart/martview
>
> My question was how to figure what type of geneID it was for 'Krt83'?
> I tried 'Ensembl Gene ID(s)' in the menu and put 'Krt83' in the box
> below it. But I get an empty mart_export.txt file.

All ensembl Ids starts with 'ENSG0....'. Your Krt83 should be an EntrezGene
id:
- http://www.ensembl.org/Homo_sapiens/Search/Details?_C=eJwFwdEJgDAMBcA3inSBKqKIA7iA*gepEcXQ1JA6v3ck4Az6Mg4!9yoOevGYT32T1Ira7hzdmOewaYmrVksceRgD6Lp9qSLoWvxUeBcJ&_c=%2b15428165997832314387&_c=%2b18088233473301975577
<http://www.ensembl.org/Homo_sapiens/Search/Details?_C=eJwFwdEJgDAMBcA3inSBKqKIA7iA*gepEcXQ1JA6v3ck4Az6Mg4%219yoOevGYT32T1Ira7hzdmOewaYmrVksceRgD6Lp9qSLoWvxUeBcJ&_c=%2b15428165997832314387&_c=%2b18088233473301975577%20>


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-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it