PC sequence

Matthew Clegg mcl at tko.vtt.fi
Tue Mar 26 02:32:20 EST 1991

In <9103251546.AA23211 at genbank.bio.net> DANJ at jhuhyg.bitnet (Dan Jacobson) writes:

>I'm looking for a program which will allow me to draw boxes around identical 
>residues in a multiple seqence alignment.

>For example in the artificial sequences below it would be nice to draw boxes
>around those residues which are identical, here denoted by an *, without 
>disturbing the sequence itself by inserting a space where the line goes 
>(which destroys the alignment).
>                         ****  ***
>                      DTCYDSKTFDCYPAT
>                      TFGYDSKLPDCYACI
>                      DYTYDSKACDCYFSR
>                         ****  ***

I wrote a program for the IBM PC several years ago which you might
find useful.  It is a sequence editor which also allows one to perform
(manual) alignment of sequences.  Matching positions are displayed on
the screen in high intensity, while nonmatching positions are
displayed in low intensity.  (If you are using a color monitor, then
two different colors are used.)  In hardcopy, matching positions are
printed in upper case, nonmatching positions in lower case.  The
editor reads several arbitrarily chosen (and probably obscure)
formats, but as far as multiple aligned sequences go, I believe it
reads the format used by Joe Felsenstein's PHYLIP package.  Actually,
this is a rather simplistic program, but you are welcome to have it if
you like.

Matthew Clegg.
Matthew Clegg
mcl at tko.vtt.fi, Mon Mar 25, 1991
Matthew Clegg
mcl at tko.vtt.fi, Mon Mar 25, 1991

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