Software to graph sequence alignments

Jerry Learn learn at SMAUG.UCR.EDU
Fri Mar 5 13:25:11 EST 1993

Kai-Uwe Froehlich responded to Bill Warren's original query:

> In <9303020004.AA14577 at umailsrv0.UMD.EDU> MAILER-DAEMON at UMAILSRV0.UMD.EDU (Mail Delivery Subsystem) writes:
> >G'day all,

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> >What I'm lookng for is a program that will take a pair of aligned
> >sequences, and plot graphically, either the similarity or identity,
> >and using a specifible window size, along the entire length of an
> >alignment. By doing this it would me far easier to see the regions
> >of high or low similarity/identity and see their relative location
> >along the length of the alignment.
> >Does anyone know of a program to do this ???
> >BILL 

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> I have no access to the GCG package, so I wonder if 
> PlotSimilarity, which has been proposed by Steve Thompson, really 
> performs the same task, summing up over a stretch of aa residues, 
> or if its graphic output rather shows single separated residues??

I can attest that Steve Thompson knows what he's talking about [at least when
he is talking about the GCG package 8-) ].  PlotSimilarity does in fact sum
over a stretch of residues.  The size of this window may be changed by the 
user.  It is a useful program for producing such a graphical output.

Jerry Learn

learn at smaug.ucr.edu
Dept. of Botany & Plant Sciences
University of California, Riverside

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