Download promoter sequence db for human genome?

ewilbanks · 10-23-2009, 12:12 AM

Hi all!

Sorry for the slightly off topic question, but....

Does anyone know where I can find a downloadable database of the promoter sequences for the human genome? Preferably as fasta files?

Thanks!

Lizzy

steven · 10-26-2009, 03:41 AM

What kind of promoters? If the upstream region of all annotated genes is ok, you can get this from UCSC/Galaxy:
From http://genome.ucsc.edu , menu:Tables, clade:mammal, genome:Human, group:genes, track: UCSC known, output: bed, "send to galaxy" box thickened. Click on "get output" and on the second screen, specify your upstream region with the "Upstream by" box (for instance 2000) and click on "send to galaxy". Then from the galaxy left menu click on "Fetch Sequences", "Extract Genomic DNA", and you should get your fasta sequences.

ewilbanks · 10-26-2009, 11:29 AM

This is perfect, thanks so much!!

steven · 10-27-2009, 10:53 AM

cool! glad i could help

btw, if anyone knows an alternative way, i am interested.
cheers,
s.

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10-23-2009, 12:12 AM	#1
ewilbanks Member Location: Davis, CA Join Date: Mar 2009 Posts: 82	Download promoter sequence db for human genome? Hi all! Sorry for the slightly off topic question, but.... Does anyone know where I can find a downloadable database of the promoter sequences for the human genome? Preferably as fasta files? Thanks! Lizzy

10-26-2009, 03:41 AM	#2
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	What kind of promoters? If the upstream region of all annotated genes is ok, you can get this from UCSC/Galaxy: From http://genome.ucsc.edu , menu:Tables, clade:mammal, genome:Human, group:genes, track: UCSC known, output: bed, "send to galaxy" box thickened. Click on "get output" and on the second screen, specify your upstream region with the "Upstream by" box (for instance 2000) and click on "send to galaxy". Then from the galaxy left menu click on "Fetch Sequences", "Extract Genomic DNA", and you should get your fasta sequences.

10-26-2009, 11:29 AM	#3
ewilbanks Member Location: Davis, CA Join Date: Mar 2009 Posts: 82	This is perfect, thanks so much!!

10-27-2009, 10:53 AM	#4
steven Senior Member Location: Southern France Join Date: Aug 2009 Posts: 269	cool! glad i could help btw, if anyone knows an alternative way, i am interested. cheers, s.