In article <scott.755199530 at phylo>, scott at phylo.life.uiuc.edu (Scott Howard)
writes:
> Shaded Annotated Sequences:
> GeneWorks and DNAStar will accomplish this. If you'd like to save
> yourself a few thousand francs, 13 point Courier and most any
> reasonably well constructed drawing program will suffice.
There is a non-commercial possibility if you are using a Macintosh - SeqApp
1.9. This does a very nice multicoloured pretty print with shading as well
as lots of other things. It was written by Don Gilbert and is free (as far
as I know). Note it is an alpha release and may cause crashes. I have
experienced these but usually they simply cause the program to quit. It's a
really nice piece of work overall. Here is Don's abstract on the program:
SeqApp is a biological sequence editor and analysis program for Macintosh
computers. It includes links to network services and external analysis
programs.
Features include
multiple sequence alignment editor
single sequence editor window
read and write several sequence file formats *
easy hand alignment features including colored bases and sliding *
automatic multiple sequence alignment thru Clustal external app
automatic gel fragment alignment to contigs thru CAP exernal app *
consensus,reverse,complement,degap operations
restriction maps
dot plots
translate dna to/from protein using various codon tables
automatic preference saving *
internet send mail, read mail
internet gopher, information retreival including genbank.
internet sequence analysis services
user-definable links to external analysis programs
and more
* These features were updated in release 1.9a. See below for details.
+++ NOTICE: This is an early, unfinished version of the program. Expect
it to fail in various ways. This release is made available to those who
wish to test and comment on its future development. This release will expire
on a date indicated in the About dialog.
SeqApp is being written by Don Gilbert, using the MacApp extensible
Macintosh programming framework from Apple Computer.
You can obtain updates of this release thru anonymous ftp to
ftp.bio.indiana.edu, in folder /molbio/seqapp, as seqapp.hqx. You may also
obtain updates directly thru an internet-connected Mac with SeqApp, using
Gopher to the IUBio archive. Look for a folder called "IUBio
Software+Data/SeqApp, Mac sequence editor". There may be additional
distribution software, data or information in this /molbio/seqapp folder.
See the Readme files in it for details.
Jim Woodgett Fax (416) 926 6529 Tel (416) 924 0671
jwoodget at ocicl.oci.utoronto.ca
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