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programs to highlight identity in MSF files

Brian Foley brianf at med.uvm.edu
Sun Dec 11 14:43:24 EST 1994

Les Klimczak (lklimcza at sas.upenn.edu) wrote:
: 	We are looking for a program that will automatically highlight
: identical and similar residues in .msf output files and that will also
: allow further editing and annotation.

Here is some documentation about Margo Haygood's Microsoft EXCEL 
macros for colorizing multiple sequence alignments.  I have used
them and they are excellent!  Some limitations, such as not
conveniently dealing with long sequences, exist, but the 
ability to modify the macros to color, shade, box or
greyscale any way you like make up for them.

this is only a small part of the README that comes with the macros:

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color sequences Version 1.0

Spreadsheet Macros for Coloring Sequence Alignments

The macros are contained in a file called color sequences.  When the file 
is opened in Excelª, a new menu (Sequence) appears on the menu bar, 
containing sequence-related commands.  The first group of commands, 
Parse Sequence and Parse Column are used in importing sequences 
into Excelª.  The second group, Color Nucleotides and Color Amino 
Acids, add colors to the sequence.  The third group of commands are 
used in highlighting regions of interest by removing or dimming 
colors in other regions.  Color Amino Acids colors most amino acids 
a different color.  The color palette was designed with reference 
to the Dayhoff log-odds matrix, which weights amino acids according 
to their observed frequency of replacement in proteins and has been 
shown to be an effective means of detecting relationships .  Amino 
acids that are heavily weighted are given the brightest colors, 
those that are more frequently replaced have less arresting colors; 
related amino acids are given similar colors.  Since Excelª's color 
palette is limited to 16 colors, a few amino acids with the lowest 
weights are colored gray.  

Color Nucleotides colors nucleotide sequence data.  The color 
palette gives purines one pair of related colors and pyrimidines 
another to reflect the typical higher frequency of transitions over 
transversions in nucleotide substitutions, and colors Gs and Cs
more intensely to communicate their stronger hydrogen bonds.  The 
colored worksheets can be printed on paper or transparencies in 
color or black and white or output as slides.

Modifying the Macros

The macro file is formatted as an international macro, so it can be used 
with international systems (the text messages will appear in English).  
The macro sheet is formatted as hidden to prevent accidental 
modification.  To view and edit the macro sheet for specialized purposes, 
choose Unhide from the Windows menu. The macros are annotated to 
facilitate modification.

Margo G. Haygood
Marine Biology Research Division and 
Center for Marine Biotechnology and Biomedicine
Scripps Institution of Oceanography
University of California, San Diego
9500 Gilman Dr., La Jolla, CA 92093-0202

Internet:      mhaygood at ucsd.edu

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Last I knew the macros were available via FTP.  They were written up
in a BioTechniques paper a few months aog.

*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *

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