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Software to graph sequence alignments

Bob Milius BMEC milius at proton.med.umn.edu
Thu Mar 4 11:20:47 EST 1993

In article <9303020004.AA14577 at umailsrv0.UMD.EDU> MAILER-DAEMON at UMAILSRV0.UMD.EDU (Mail Delivery Subsystem) writes:
>G'day all,
>I guess that there are very few molecular biologists who have never
>had the need to produce an optimal seqeunce aligment or at least
>needed to look carefully at one. There are indeed many different
>programs available that optimise these seqeunce alignments, the
>output of which is usually a series of aligned character strings
>with gaps in appropriate places and special characters to denote
>identity or similarity.
>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 ???

The GCG package contains a program called PLOTSIMILARITY that does what
you want.

Also I've written a program that I'm calling ZGOR that uses the algorithm of
Zvelebil, M.J., et al.  J. Mol. Biol 195:957-961  (1987). It takes a
family of aligned protein sequences, calculates the conservation index 
for each position based on Taylor's Venn Diagram of amino acid structural 
relatedness, then calculates the average GOR secondary structure prediction
weighed at each position based on the conservation index. It's still pretty
crude, but it seems to work. It's written in ansi C and has been compiled
on my Mac using Think C and on the SGI. The output is a tab deliminated
text file which can be read by most spreadsheets such as Excel for plotting.
It uses Don Gilbert's ReadSeq library routines to read in the sequences. 
I've only tested it on MSF format files. If you're interested, drop me a note.

Bob Milius
Biomedical Engineering Center
University of Minnesota
milius at lenti.med.umn.edu
(612) 626-2614

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