Dear Klaus, You could make a dot-plot of the sequence against itself. Repeats will show up as diagonal lines parallel to the main diagonal.
http://emboss.sourceforge.net/apps/cvs/emboss/apps/dotmatcher.html best wishes James -- Dr. James W. Murray David Phillips Research Fellow Division on Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 ________________________________________ From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Tim Gruene [...@shelx.uni-ac.gwdg.de] Sent: Friday, June 04, 2010 11:09 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Displaying repeats in a amino acid sequence Dear Klaus, would the SMART-Server (http://smart.embl-heidelberg.de/) be something you are looking for? If your repeats are long enough to make up domains it might. Tim On Fri, Jun 04, 2010 at 08:15:03PM +0000, Klaus Sengstack wrote: > Dear all, > > I am looking for an alignment program that is able to display repeating units > in the sequence. In the C-terminus of my protein I found some specific > repeats which I want to visualize. Does anybody know such program? Thanks a > lot. > > Best regards, > K.Sengstack > > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
