Path: utzoo!utgpu!news-server.csri.toronto.edu!rpi!zaphod.mps.ohio-state.edu!wuarchive!uwm.edu!bionet!bio.embnet.se!sunic!news.funet.fi!ousrvr!mcl@tko.vtt.fi From: mcl@tko.vtt.fi (Matthew Clegg) Newsgroups: bionet.software Subject: Re: PC sequence Message-ID: Date: 26 Mar 91 07:32:20 GMT References: <9103251546.AA23211@genbank.bio.net> Sender: news@ousrvr.oulu.fi Organization: University of Oulu, Finland Lines: 36 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