William_D_WARREN at umail.umd.edu in Message-Id:
<9303020004.AA14577 at umailsrv0.UMD.EDU> writes:
>...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....
If you have access to GCG, their program PlotSimilarity does exactly this.
It will also deal with multiple sequence alignments and has many built-in
options as well as being able to take advantage of the extensive graphics
capabilities of the Figure program.
Happy plotting, Steve T
Steven M. Thompson
Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
Washington State University, Pullman, WA 99164-1224, USA
AT&Tnet: (509) 335-0533 or 335-3179 FAX: (509) 335-0540
BITnet: THOMPSON at WSUVMS1 or STEVET at WSUVM1
INTERnet: THOMPSON at wsuvms1.csc.wsu.edu