[BiO BB] Getting sequences by base pair locations

Cook, Malcolm MEC at Stowers-Institute.org
Fri Jul 28 12:19:42 EDT 2006

There are many options.
But, it looks like you only have start end coordinates!  Where do you
know which chromosome/contig the hit was on?
Assuming you have this, if you did the blat with a local copy of the
blat program and a the genome, then in addition to the blat command, you
have the twoBitToFa command which can extract the hits from the blat
index (see http://genome.ucsc.edu/goldenPath/help/blatSpec.html)

Or did you do the blat at ucsc?

Malcolm Cook
Database Applications Manager, Bioinformatics
Stowers Institute for Medical Research  


bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at bioinformat
ics.org] On Behalf Of Yuval Itan
	Sent: Thursday, July 27, 2006 11:23 AM
	To: bio_bulletin_board at bioinformatics.org
	Subject: [BiO BB] Getting sequences by base pair locations
	Hello all, 

	I was BLATing a few hundred human genes against the chimp
genome, and kept the best chimp hits for every human gene. 
	I have the base pair start and end location for every chimp hit,
and I need to get the sequence for each of these chimp hits. Here is an
example for a few chimp hits bp locations: 

	Start End 
	142854 144504 
	154479 155198 
	153066 167370 
	163146 163559 
		I have one chimp genome file (about 3GB) including all
chromosomes, but I could also get one file per chromosome if that would
make things easier. Does anyone have a script or a link for an interface
that can do the job? 

	Thank you very much, 


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