The disadvantages of several "homespun" programs that visually enhance
sequence alignments are that: 1, they use quite primitive or ill-defined
algorithms; 2, they cannot be easily configured; 3, the final output cannot
be modified/graphically enhanced. We use here Excel macros that were
originally developed for coloring sequence alignments [Haygood MG (1993)
Spreadsheet macros for coloring sequence alignments. Biotechniques 15:
1084-1089; available at ftp://sio.ucsd.edu/haygood/color*]. I have
re-programed these macros to convert the lowercase output of Pretty -CASE
(non-similar) to normal uppercase and the uppercase output (similar) to
uppercase on gray background, and then to identify identical residues by a
reverse font (black background/white letters). Anybody who has a rudimentary
understanding of macro programing can customize them according to their
needs.
This procedure is thus based on the well-defined, high-level algorithms
of GCG, and the macros provide only graphical enhancement of the alignment.
The output is an Excel spreadsheet, which can be easily configured with
regards to font type and size, can be annotated, or even moved to a graphic
application (e.g. Canvas) for further enhancement.
After testing virtually all the programs out there, I find this approach
the most versatile and satisfactory.
Les
_____________________________________________________________________
Les J. Klimczak | INTERNET: lklimcza at sas.upenn.edu
Department of Biology |
University of Pennsylvania | Tel.: (215) 898 3673
Philadelphia, PA 19104-6018 | FAX: (215) 898 8780
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