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

[Giovanni Marco Dall'Olio]

I suppose it is Flank(Transcript), with upstream=5000 and downstream=5000
-
http://www.ensembl.org/biomart/martview/7675ba9923b086fb5d3a76f753cd5c98/7675ba9923b086fb5d3a76f753cd5c98

it seems you have to execute the query two times, one for upstream and one
for downstream.


On Wed, Oct 28, 2009 at 11:20 PM, Peng Yu <pengyu.ut at gmail.com> 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'.
>
> 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
> >
>
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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