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

[Peng Yu]

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'.

If I want both 5kb upstream of TSS and .5kb downstream of TSS, is
there a way to do so?


> As for doing that in python, I am not sure there are python interfaces
> to BioMart. Galaxy (http://main.g2.bx.psu.edu/) is written in python,
> so they must have written a library for that somewhere, but I don't
> know their code.
>
> If you use R (remember that you can mix python and R with rpy2) there
> is a nice module in bioconductor called BioMart.
>
>
>> I have the following specific questions. Could somebody help me? Thank you!
>>
>> Which database I can access to get mouse genome?
>> Give a gene name what function I should call to get the gene's location?
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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
>