Another useful diagonal dot-plot program is Dotter by Erik Sonnhammer and Richard Durbin which can be downloaded from
http://sonnhammer.sbc.su.se/Dotter.html This has a useful "GreyRamp tool" to interactively change the level at which the dots are drawn. You can click on the plot and see the local sequence alignments... best wishes Pete On 5 Jun 2010, at 07:22, Murray, James W wrote: > 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 Prof Peter Artymiuk Krebs Institute Department of Molecular Biology & Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND
