[BiO BB] Extracting upstream sequence of a gene

[Maximilian Haeussler]

(Kind of late reply.)

There are various methods. Biomart is one of them.

But you can do the same thing with the UCSC browser.

You have two options here:

a) download directly from their website (they have
upstreamxxxx.zip-files prepared for you!)

e.g. for mouse: http://hgdownload.cse.ucsc.edu/goldenPath/mm7/bigZips/

b) with the table browser (I quote an old mail from Jen from UCSC):

Using the Table browser form ("Tables" in blue navigation bar):
1. Select genome/release = mm7, group/track = RefSeq, region=genome
2. Output = sequence, type in a file name, select .gzip compression
3. On next page sequence type = genomic
4. And on final page specify the amount of upstream sequence

good luck,
Max

> Here is the link to Biomart:
> http://www.ensembl.org/Multi/martview
>
> Steps:
> 1) Under Dataset:
>    -Selected (ensembl 38, homo sapiens genes )
> 2) Filters:
>    -GENE
>       - ID LIST LIMIT - "HGNC Symbols", Enter symbols or upload a list.
> 3) OUTPUT
>    - ATTRIBUTE - (Select Sequences)
>    - SEQUENCES - (Select Flank(Gene))
>    - Check box "Upstream Flank"
> Choose as many other attributes as you need in your output file.
>
>
> -Kiran
> Quoting Paulo Nuin <pnuin at terra.com.br>:
>
> > Hi
> >
> > If you have the IDs of these genes you can do that on the UCSC genome
> > browser. You can set a region to download automatically from a multiple
> > search.
> >
> > Regards
> >
> > Paulo
> >
> >
> > kannaiah at bsd.uchicago.edu wrote:
> > > Hello,
> > >
> > > I have seen a few posts asking similar questions. I am looking to do
> > something
> > > similar too.
> > >
> > > I want to extract the upstream sequence of genes (upto 3000bp upstream)
> > in
> > > Human. But going thru the ensembl website is ok, if one has few genes.
> > >
> > > But i have a few hundred genes. I was wondering what would be the best way
> > to
> > > automate this.
> > > Should i try blasting the gene sequences to the Human Chromosome files, and
> > then
> > > parse the blast output to get the position of the genes, and go back and
> > read
> > > the chromosome sequence where it was found and get the upstream sequence.
> > >
> > > That would be a long way, hopefully there is someother shorter way to do
> > this,
> > > which i am not aware of.
> > > Any suggestions would be welcome:)
> > >
> > > Thank you
> > >
> > > -hak
> > >
> > >
> > >
> > >
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-- 
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
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