downloading promoter sequence for string search

[Jessilyn Dunn]

Hello,

I am trying to use the UCSC browser to download the DNA sequence for gene promoters (+/-1kb from TxStart).

To do this, I planned to download the sequences using the table browser (RefSeq genes track) by defining +/-1kb from the TxStart using the "region," but I do not see a way to define this. Alternatively I created a "position" file in bed format containing the genomic coordinates of all promoters, but it has ~34,000 lines and it appears the limit for user-defined regions is 1,000. There must be a better way to do this, but I'm not sure how.

My overall goal is to get all of the gene accession #s for genes with a specific transcription factor binding sequence in their promoter. I also see that there is a potentially a method under "filter constraints" where I could do a string search within a sequence set, rather than exporting the sequences and writing code to do this.

Any insight you can provide on better methods would be greatly appreciated!

Thank you very much!

Sincerely,

Jessilyn

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Jessilyn Dunn

NSF Graduate Research Fellow

Jo Lab of Vascular Mechanobiology and Disease

Dept. of Biomedical Engineering

Georgia Institute of Technology & Emory University