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:
ftp://ftp.mcs.anl.gov/pub/overbeek/PatScan
Finally, if you have inverted repeats of defined sequence, you could
use Harry Mangalam's tacg2 program. Available from:
http://hornet.mmg.uci.edu/~hjm/projects/tacg/tacg2.main.html
Cheers,
Ashok
--
Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
http://aiyar.cjb.net
