Software to display sequence alignments

Geoff Barton gjb at bioch.ox.ac.uk
Wed Mar 10 09:39:06 EST 1993

Kai-Uwe Froehlich writes...

> Confronted with the problem to produce a graphical output of 
> aligned sequences for an easy visualization of more and of less 
> similar regions, I devised a method which displays the degree of 
> similarity in grades of gray. Each aligned sequence therefore is 
> presented as a bar filled with stripes of different darkness. It ...
... lots of details deleted..

I also have been confronted with the general problem of visualising
sequence alignments.  My particular solution is the program ALSCRIPT
briefly described in: Protein Engineering, 6,37-40, 1993.  ALSCRIPT
takes a sequence alignment and turns it into PostScript which can then
be printed, or viewed on a workstation or PC using a PostScript
previewer.  The program automatically splits large alignments onto
multiple pages which can be pasted together, it allows boxing,
shading, colouring (of characters/backgrounds), arbitrary text, mixing
of different fonts and pointsizes.

ALSCRIPT is simply a tool for formatting the alignment, it does not
decide for you what should be shaded/boxed.  These analysis functions
are left either to manually entering the necessary commands, or to
other programs written to produce ALSCRIPT commands.  Our own
particular bias in the analysis of alignments is to shade/box
according to conservation of the physico-chemical properties of the
amino acids.  We hope to distribute a program (AMAS) that implements
these ideas later this year (Livingstone and Barton, 1993, submitted).

Since ALSCRIPT takes care of the problems of graphical layout, and
provides a command interface, different methods of "highlighting" an
alignment may rapidly be implemented as stand-alone programs that
produce ALSCRIPT commands.  The requests for grey-bar highlighting, or
similar representations could be easily handled by the ALSCRIPT
interface.  One could even alter the size of the font, or colour, or
font type, according to similarity,!

I am distributing ALSCRIPT for academic, teaching and non-commercial
use.  Commercial users should write for details of the commercial

If you would like a version for Unix machines, then I can ftp a
compressed tar file to an account of your choice.  I am also
distributing a version for MS-DOS (386 machines or better).  If you
would like the MS-DOS version (identical to the Unix version, but
including binaries), then please send a formatted 3.5" disk together
with suitable packaging for its return and a return address label.

The current version is 1.4.3.

Geoff. Barton

Internet:    gjb at bioch.ox.ac.uk      (Janet:  gjb at uk.ac.ox.bioch)

Telephone: [44] (0)865 275368    [ ] Delete when dialling from UK.
Fax:       [44] (0)865 510454    ( ) Delete when dialling from outside UK.

           Dr. Geoffrey J. Barton     
           Laboratory of Molecular Biophysics
	   University of Oxford
           Rex Richards Building
           South Parks Road
           Oxford OX1 3QU

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