blast of the 454 reads

[dina]

Hi
I want to find virus integration sites in a genome we sequenced. Is it more reasonable to blast the resulted contigs or maybe blast the reads themselves would be more productive?
Do you have any other idea how to "catch" those integration sites?
Thank you!

[bioinfosm]

Assembly into contigs will iron out some of 454's noise and give better results I guess. BLAT might be a faster option than blast!

[dina]

Blat

Thank you. Can you explain to me how do I run BLAT for mant contigs as abatch? how I can do that via the command line and not on the web? Thank you!

[bioinfosm]

You may try UCSC with some of your contigs to see how it works

http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Then probably install blat locally and use their command line..