programs to highlight identity in MSF files

Margo Haygood mhaygood at ucsd.edu
Mon Dec 12 12:46:33 EST 1994

Thanks for Brian Foley's kind words about my Excel macros for coloring
sequence alignments. I have had several inquiries in response to his
message. Instructions for obtaining the macros follow:

The macros were written in Excel 4.0.  I haven't gotten around to
upgrading to Excel 5.0, and so I don't know how they will behave in the
new version.  If anybody tries it, let me know how it goes.  Some of the
limitations, such as line length, are inherent in Excel, and I hope they
have been improved in the new version.

For those who haven't read the article (Haygood, M.G. 1993. Spreadsheet
macros for coloring sequence alignments), please read the file "about
macros"  It is an abridged version of the article and explains some of the
tricky aspects. 

Obtaining the Excel macros (in the mac style of compressed file) for
coloring sequences:

By Gopher:

Connect to the server sio.ucsd.edu navigate to the directory
SIO-Department/MBRD/haygood and thenjust double click on the file to
retrieve it.

By anonymous ftp:

ftp to sio.ucsd.edu, login as anonymous with email address as the
password.  The files are in the directory Haygood.  Ftp should be in 
binary mode.

    The file color_macro.sea.hqx is a BinHex 4.0 file of a 
self-extracting archie containing the Excel macros, a readme and
a set of test files. Depending on the software you use to get it you may
need to use BinHex 4.0 to process the file.  Then just double click on it
and it will self extract.

For difficulties obtaining the files from sio.ucsd.edu, contact John
Studarus at jstudaru at sdcc5.UCSD.EDU

For questions about the operation of the macros contact Margo Haygood at
mhaygood at ucsd.edu

For PC users:

We have put up a PC accessible file (a self-extracting .exe file, it is in
the same location). At the moment, the macro file it creates need to be
renamed as color.xlm.  The .xlm extension allows Excel to recognize it
immediately as a macro file.  The next one we put up will do that

Excel for Windows 5.0 displays colors correctly, earlier versions have a
bug that causes the colors to display less nicely on a PC than they do on
the mac (the actual file is unaffected because if you transfer back to the
mac the file displays fine).  I don't know if it affects output. On the up
side, the macros run much faster on a PC.  Even for mac users, for really
large files it can be worth it do to the coloring on a PC and transfer
back to the mac.

If you can't access by gopher or ftp, contact me again.

In article <1994Dec11.194324.5619 at emba.uvm.edu>, brianf at med.uvm.edu (Brian
Foley) wrote:

> 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.

> 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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