PC sequence/boxed alignment

hill at mcclb0.med.nyu.edu hill at mcclb0.med.nyu.edu
Wed Mar 27 15:17:06 EST 1991

Another suggestion about making boxed alignments is to do it in two
stages: use an alignment program to do the alignment and a graphics
program/word processor to make the figure.  My standard procedure is to
create the alignment (on the VAX using the GCG programs or on a DOS
machine using PC/GENE but any method that produces ASCII files would
work), transfer it to the Mac, and use Nisus (3.05) on the Mac to create
the final figure.  Nisus works particularly well because it is a word
processor with both powerful text editing capabilities and graphics
capabilities, but other programs will work.

One thing to remember is that most Macintosh word processors use a
proportional font as the default.  Thus, when you open your ASCII
alignment on the Mac, the sequences will not appear aligned.  Select the
entire alignment and change the font to Courier or some other
monoproportional font (plus you may have to change the size of the font
and/or the margins), and everything will be aligned again.

I realize that this solution is not as elegant as one program that does
it all, plus it requires transferring the file betweeen computers.  In
balance, however, it means that you probably already know how to do the
graphics on your Mac or PC and you may be able to do more sophisticated
figures by capitalizing on the strengths of each program.

Disclaimer: my only connection with Nisus, GCG, or PC/GENE is as a very
satisfied user.  In the case of Nisus it extends to the great
educational pricing for the individual user.

John Edward Hill, Ph.D.            |  Department of Cell Biology             
Internet: HILL at MCCLB0.MED.NYU.EDU  |  New York University Medical Center
  EARN/Bitnet: HILL at NYUMED.BITNET  |  550 Fifth Avenue                  
212-263-7135    FAX: 212-263-8139  |  New York, New York  10016-6402

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