[BiO BB] Getting sequences by base pair locations

Liangyou liangyou at gmail.com
Sat Jul 29 18:06:03 EDT 2006

What do you want to automate?  The whole process including: blasting
all sequences from a database of sequences, getting the start and end positions
of the best hits, and getting the sequence for each hit?  Or just want
to get the sequence for each hit?

If you want to do the whole process and you know how to get the
sequence for each hit (either from a Web interface, or you have a
standalone program to extract the sequence from the genome) I may help
you to set up
a script.  It is just needs a couple of hours to do so.


On 7/27/06, Yuval Itan <y.itan at ucl.ac.uk> 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?
> Thank you very much,
> Yuval
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