Question: Obtaining A Fasta With Conserved Region Near A Gene In Ucsc Genome Browser
gravatar for Anima Mundi
9.1 years ago by
Anima Mundi2.5k
Anima Mundi2.5k wrote:


I would like to obtain, from UCSC Genome Browser, a FASTA with 5 Kb upstream the promoter plus intron regions of a gene of interest; how can I obtain only the conserved sequences among different species (those proposed by the tool), instead of generating a FASTA with the whole 5 Kb upstream plus the whole intron regions? Thanks in advance.

gene fasta conservation ucsc • 2.4k views
ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 9.1 years ago by Anima Mundi2.5k

This is helpful, thanks again.

ADD REPLYlink written 9.0 years ago by Anima Mundi2.5k
gravatar for Treylathe
9.1 years ago by
San Francisco
Treylathe950 wrote:

Someone will propose a more elegant coding solution, but in the meantime if you just want to do this 'quick and dirty', I'd suggest the Table Browser intersection function or Galaxy join function. I can give you a more complete step-by-step, but it might have to wait till I'm at my computer and not my iPad :D.

Edited to add:

can't promise much more than this at the moment, got busy and travel coming up :D... but here's the basic outline that I think will work. I'm sure there is a more elegant solution. Use Table Browser Choose UCSC Known Genes (use whatever gene position, IDs you have as position) Create custom track Choose "introns" or "upstream (5000kb) create track

Create a second track Choose conservation in comparative. There are many to choose from, look at the documentation to determine which (across vetebrates, mammals, etc) Filter for a value you prefer for conservation (again, look at documentation) create a second custom track.

In Table Browser choose first custom track, intersect with second custom track get sequence as output

That should get you a FASTA record of only those regions that have an overlap with a high conservation score you choose. I'm sure there must be a more elegant way (and to get very specific regions) than this, but that's the 'quick and dirty' method.

ADD COMMENTlink modified 9.0 years ago • written 9.1 years ago by Treylathe950

I would be glad to read and try your step-by-step tutorial. Thanks,


ADD REPLYlink written 9.1 years ago by Anima Mundi2.5k
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