DANJ@jhuhyg.bitnet (Dan Jacobson) (03/25/91)
Hi,
I'm looking for a program which will allow me to draw boxes around identical re
sidues in a multiple seqence alignment.
For example in the artificial sequences below it would be nice to draw boxes ar
uond those residues which are identical, here denoted by an *, without disturbi
ng the sequence itself by inserting a space where the line goes (which destroys
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 IBM
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.
Sincerely,
Dan Jacobson
danj@jhuhyg.sph.jhu.edu (internet)
danj@jhuhyg (BITNET)mcl@tko.vtt.fi (Matthew Clegg) (03/26/91)
In <9103251546.AA23211@genbank.bio.net> DANJ@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@tko.vtt.fi, Mon Mar 25, 1991 -- Matthew Clegg mcl@tko.vtt.fi, Mon Mar 25, 1991
elliston@av8tr.UUCP (Keith Elliston) (03/28/91)
In article <9103251546.AA23211@genbank.bio.net>, DANJ@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@av8tr.UUCP elliston@msdrl.com AA5A N9734U elliston@mbcl.rutgers.edu elliston@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'
ahouse@BINAH.CC.BRANDEIS.EDU (Jeremy Ahouse) (03/29/91)
In article <9103251546.AA23211@genbank.bio.net>, DANJ@jhuhyg.bitnet (Dan Jacobson) writes: > >I'm looking for a program which will allow me to draw boxes around identical re >sidues in a multiple seqence alignment. >DOS system is preferable but a MAC would be OK too. The third option is an IBM On the mac the word processor called Nisus will accomplish what you want (v 3.05). It also allows you to use inverted type. Good luck - Jeremy --------------------------------------------- / Jeremy Ahouse / Brandeis University / Biophysics / Waltham, MA 02254-9110