percent value for local alignements

Steve Thompson stevet at wsu.edu
Mon Sep 29 13:44:59 EST 1997

In Article <342A0F3B.17638003 at no.spam.kuleuven.ac.be>, dodo
<nowhere at to.find> wrote:
>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
>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

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