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Software to graph sequence alignments

Dan Jacobson danj at welchgate.welch.jhu.edu
Tue Mar 2 11:35:22 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 ???

You might want to take a look at Maligned (written by Steve Clark).
Maligned allows you to create alignments manually (or input alignments
from some of the other alignment programs) and gives you on-screen shading
of the alignment based on identity or similarity.  As you shift a sequence
you can see the shading change and zero in on better alignments.  Maligned
will also give you statistics on an alignment - including the percent
identity at each position in the alignment - you can easily feed that
into an XY plotting package or a spread sheet and get the type of
graphical display you thinking of.  Maligned is designed for multiple
alignments and can handle 200 sequences at a time if you'd like.
Maligned runs under VMS and is available from (among other places)
ftp.bio.indiana.edu by gopher or anonymous ftp in the molbio/vax

Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu


A clip from the Readme file is as follows:


	MALIGNED stands for Multiple ALIGNment EDitor. Is is a screen
editor designed to demonstrate sequence similiarity between related genes
or proteins. The regions of similarity in each sequence are highlighted;
the screen is updated to reflect the current similiarity as the alignments
are changed by shifting a sequence relative to the others, or by adding
gaps. This constant visual feedback of the overall alignment makes it easy
to see the effect of changing the alignment. 

     MALFORM is a post-processing program that converts the ".MAL" file 
produced by Maligned to a file that can be printed on a postscript printer. 

	Maligned and Malform run on a VAX/VMS system and were compiled and
linked under VMS v5.3-1. These programs and files are copyrighted by
Stephen Clark, 1992 (c), but may be freely distributed so long as all files
are distributed and without any changes, and no fee is charged. Once
obtained, the configuration, help and document files may be edited to make
them conform to the local environment, and may be further distributed for
the benefit of others with the same output devices. 

	A paper describing Maligned is in press in CABIOS ("Maligned: a 
multiple sequence alignment program," by Stephen P. Clark.)

	Comments, suggestions, bug reports, etc, can be sent to me at the 
indicated address (Internet is prefered).

Stephen Clark                           May 17, 1992

clark at salk-sc2.sdsc.edu  (Internet)
clark at salk               (Bitnet


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