PC sequence

[Keith Elliston]

In article <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 r
> sidues in a multiple seqence alignment.
> 
> For example in the artificial sequences below it would be nice to draw boxes a
> uond those residues which are identical, here denoted by an *, without disturb
> ng the sequence itself by inserting a space where the line goes (which destroy
> the alignment).
>                          ****  ***
>                       DTCYDSKTFDCYPAT
>                       TFGYDSKLPDCYACI
>                       DYTYDSKACDCYFSR
>                          ****  ***
> 
> Surely some of the alignment programs can do this.  One which will run on a PC
> DOS system is preferable but a MAC would be OK too.  The third option is an IB
> mainframe running VM/CMS.
> I'd appreciate any information that you can provide, be it the program name or
> an FTP site which holds it.  Thanks.

This can very easily be done using microsoft excel.  You can draw borders 
around your individual or group residues, make residues bold or larger than
the others, and if you happen to have a color output device, you can print
different colors for classes of residues.  

I have done this extensively on my mac, and an example of such an alignment,
complete with color, can be found in the following reference:

Wiederrecht,G. Brizuela, L., Elliston, K., Sigal, N. and Siekierka, J. 
"FKB1 encodes a nonessential FK 506-binding protein in Sacharomyces
cerevisiae and contains regions suggesting homology to the cyclophilins."
Proc. Natl. Acad. Sci. USA  88:1029-1033. 1991.

(I couldn't help joining in the latest bionet craze of citing ones own work!!)

Anyway, you can automatically load the output from several multiple sequence
alignment programs (like clustal) by placing a tab between every character
in the alignment, and then pasting this into excel.  I wrote myself a simple
hypercard script to do this, but you can do it any way you like.  Then, just
edit the alignment to your hearts content, with one residue per cell.

Good luck.

Keith Elliston


-- 
Keith O. Elliston          elliston at av8tr.UUCP           elliston at msdrl.com
AA5A N9734U                elliston at mbcl.rutgers.edu     elliston at biovax.bitnet
"Beware of pseudo-experts with a mission and a grudge, especially if they are
 lawyers pretending to be scientists." -- H.W. Lewis in 'Technological Risk'