program that finds repetitive sequences

[Jeffrey Keen]

It probably depends how much sequence you have to deal with - I do a
BlastX search against a database of Alu translations using the NCBI Blast
server then parse the result file and raw sequence with J-M Claverie's
XBlast program (available from the NCBI ftp-server).

XBlast substitutes an N (or any other character) in the regions of Alu homology.
A little tedious for a lot of sequence, but it works really well.

Jeffrey Keen
j.keen at ucl.ac.uk

In article <415u33$535 at nntp3.u.washington.edu>, gregs at u.washington.edu
(Greg Schaefer) wrote:

> Hello,
> 
> I'm looking for a program that can find repetetive sequences in DNA.
> 
> In the best world it would also tell me the spots where it found them.
> 
> Anyone know of such a thing?
> 
> Thanks,
> 
> Greg