3'UTR Strip from all genes

Question

[josolvason]

Hi,

I am interested in stripping the sequences of 3'UTRs of all genes from the UCSC genome browser. So far I've been toying around with cruzdb. Its simple enough to do with the genome browser GUI (browser -> search gene -> knownGene -> genomic sequence -> click only 3' UTR -> sequence.fasta). I assume since I can filter using a GUI I can also code this into python through an API? Not necessarily looking for an answer here, but direction would be greatly appreciated. Also, I'm keen on avoiding abuse of the ucsc server. Go Slugs!

Thanks,

Joe

[GenoMax]

It should be possible to do using mysql and right queries at UCSC or by using BioMart at Ensembl via API or R.