output of alignment

CashSlave user at sas.upenn.edu
Thu May 25 15:44:47 EST 1995

    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 
   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 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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