[Bioperl-l] Getting sequences by base pair locations

Yuval Itan y.itan at ucl.ac.uk
Tue Aug 1 09:36:20 EDT 2006


Thank you all for all the helpful answers!
Malcolm- I've used the UCSC server to do the BLAT search (because I 
couldn't run it locally due to memory problems)- so I could not get the 
chimp sequences in a convenient way. I have the results also in a 
normal Blat output including all usual fields: chromosome number etc.
Wade- thanks a lot for your offer, that would be great. The chimp 
genome is just one large fasta format file.
Cheers,
Yuval
On 28 Jul 2006, at 14:30, Sean Davis wrote:

> Yuval Itan wrote:
>> 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?



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