Local BLAT Install?

[Serrao, Erik A.]

Hello,

I am a postdoc at Harvard Medical School, and I would like to use BLAT to align thousands of individual human DNA sequences. Can you please suggest a method to do this as efficiently as possible? I am not very programming-literate, but I have heard that doing a local BLAT install may be a good idea. Would you be able to walk me through this or offer other useful ideas?

Thanks so much,

Erik


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Luvina Guruvadoo]

Hi Erik,

Thanks for your question. For large batch queries, we recommend downloading BLAT and running it locally. Please see the following links for more information:
http://genome.ucsc.edu/FAQ/FAQblat.html#blat3
http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads

Also, here are a couple of help pages:
http://genome.ucsc.edu/goldenPath/help/blatSpec.html
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

- - -
Luvina Guruvadoo
UCSC Genome Bioinformatics Group