In Article <342A0F3B.17638003 at no.spam.kuleuven.ac.be>, dodo
<nowhere at to.find> wrote:
>Hi!
>I hope I can explain what I want. I am comparing to proteins that have some
regions that are 100%
>identical, some that are variable etc. What I would like to do is a graph that
shows a schematic
>diagram of teh aligned proteins (NOT THE SEQUENCE) and then say that this
region has such a identity
>and that region such etc. Now, BLAST or FASTA give me an overall percentage
identity but not a local
>one. Since both proteins are >1000aa, I would prefer not to count by hand the
percentages.
>So, the question is: does anyone know a program that would give me local
percentages (say in blocks
>of 100aa)?
Hello Przemko -
Have you tried GCG's PlotSimilarity - sounds like exactly what you want. It
uses a user specified window to plot the running similarity along a group of
aligned sequences. If you want identities rather than similarity, just use
its identity option. I use this program a LOT and really like it.
- Steve
Steven M. Thompson
Consultant in Molecular Genetics and Sequence Analysis
Visualization, Analysis & Design in the Molecular Sciences (VADMS)
Washington State University, Pullman, WA 99164-4660, USA
AT&Tnet: (509) 335-3179 FAX: (509) 335-9688
INTERnet: thompson at ribozyme.vadms.wsu.edu
