GeneDoc Beta: Program for .msf files for MS/Win

ketchup Ketchup at cris.com
Wed Feb 28 16:29:41 EST 1996

I'm looking for beta testers to give me feedback on a program
that works with Multiple Sequence format  files. This program could be
considered an extension of the  "maligned" program. There are
currently only MS Windows versions and it is still in its infancy.



GeneDoc's features include:

Three different display modes which help focus attention on different
important aspects of multiple sequence alignments.

     Conservation mode focuses attention on residues that must remain
constant or nearly so to maintain the functional and structural
integrity of the molecule. 
     Differences mode focuses attention on variable regions in the
sequence which can be important in adapting to new environments or the
evolution of a new function. 
     Quantify mode focuses attention on the pattern of changes in
different variable positions. This provides an indication of the
consistency with which different positions in the sequence reflect the
same evolutionary history. 

Scoring function allows quantitative evaluation of whether alignment
changes are improving or degrading the alignment.

Widely used similarity scores for both proteins and nucleic acids are
built in.

Calculation and display of consensus sequences. 

Objective definitions of what substitutions are conservative based on
positive scores in amino acid and nucleotide similarity tables.

The user can define groups of residues to be treated as equivalent for
highlighting purposes.

Complete user control of highlighting. 

     Up to three user definable levels that can be applied
     Manual highlighting (or removal of highlighting) at the
individual residue level. 
     Highlighting in either color or gray scale. 

Subsections of an alignment illustrating specific or special points
can be easily created and saved independently without disturbing the
main alignment.

Annotation can be added, by the user, either above or below the

Sequences can easily be added, deleted or reordered within the

Uses the widely used Genetics Computer Group (GCG) .msf multiple
sequence file format for convenient import and export of alignments.

Flexible page layout for printing and publication as well as control
of the font, the font size, and other font attributes.

Copy function to put highlighted and annotated alignments into word
processing programs or presentation programs.

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