How to find (imperfect) repeats in DNA sequences ?

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Tue Jan 19 22:39:11 EST 1999

On Fri, 15 Jan 1999 16:30:08 GMT,
    Georg Lipps (Georg.Lipps at uni-bayreuth.de) wrote:
>Hello everybody,
>I have a 5kb DNA sequence and would like to analyze the direct and
>inverted repeats on it. Is there a computer programme or a Webservice
>available to perform this task ?

You can find direct repeats using a program such as Erik Sonnhammer's 
Dotter (ftp://ncbi.nlm.nih.gov/pub/esr/dotter)

For inverted repeats, you can use Michael Zuker's DNA mfold server
available on the web at http://mfold1.wustl.edu/~mfold/dna/form1.cgi
If you have MFOLD-2.3 installed on your computer, you could also use 
it with NA set to DNA.

Another fast alternative to identifying inverted repeats (or any other
patern) is Ross Overbeek's "scan_for_matches".  Available from:

Finally, if you have inverted repeats of defined sequence, you could
use Harry Mangalam's tacg2 program.  Available from:

Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research

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