Highlighting Sequence Alignment

[Mick Partis]

Stu Johnston <sjohnston at watson.princeton.edu> wrote:
>I am making a sequence alignment figure and would like to highlight(in 
>black and white) the conserved regions between the different sequences.  

>
>Does any know of any available programs which will do this highlighting 
>automatically and how I might obtain a copy?  Or recommendations on the 
>best way to construct such a figure?
>
>Thank you


I have been impressed by genedoc which is available at 
http://www.cris.com/~ketchup/genedoc.shtml  the program accepts .MSF 
files from GCG pileup, or files in fasta format.  Runs under windows and 
does everything you want and then some more!

Alternatively you could use boxshade, which is on several of the main 
archives (try ebi http://www.ebi.ac.uk/biocat/biocat.html)

Mick

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