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
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Dr. James W. Murray
David Phillips Research Fellow
Division on Molecular Biosciences
Imperial College, LONDON
Tel: +44 (0)20 759 48895
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From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Tim Gruene [[log in to unmask]]
Sent: Friday, June 04, 2010 11:09 PM
To: [log in to unmask]
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
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