program that finds repetitive sequences

[Borries Demeler]

In article <415u33$535 at nntp3.u.washington.edu>, Greg Schaefer
<gregs at u.washington.edu> 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? 
>

Greg, I might just have what you are looking for. I used a program called
"frep" (=find repeats) by Jim Holloway to look for repeats of desired
lengths in 16S rRNA. As input, you need a sequence file (ascii format, can
be any string, not just DNA or RNA), a given repeat length minimum and
maximum, and a cutoff for the number of repeats returned. It usually 
doesn't make sense to look for short repeats, since they occur too 
frequently, hence the minimum cutoff. The program will print out the 
repeat sequence, the sequence positions, and all subsets of the sequence.
It comes with a test file after which you can model your input file. The 
program can be found on my anonymous ftp server:

ftp://bioc02.uthscsa.edu/pub/unix/sequence/frep.tar.gz

it's a gnu-zipped tar archive, and compiles cleanly with gcc on my linux 
box. To unarchive, type:

tar -xvzf frep.tar.gz

then make clean;make frep.

For additonal info look at frep.c, or contact Jim Holloway. Last e-mail 
address I had was holloway at ava.bcc.orst.edu

Hope that helps you out.

Regards, -Borries

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Borries Demeler
University of Texas Health Science Center
Department of Biochemistry
7703 Floyd Curl Drive
San Antonio, Texas 78284-7760

Phone: (210) 567-6592
Fax:   (210) 567-6595

E-mail: demeler at selway.umt.edu, demeler at bioc02.uthscsa.edu
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