GeneDoc 1.07 available: MS/Win program for .MSF files.

Ketchup Ketchup at cris.com
Sun Mar 10 19:38:01 EST 1996

Genedoc version 1.0.007 is available at:


or via anonymous ftp at

ftp://ftp.netcom.com/pub/ka/karl/gd107.exe  (16 bit version)
ftp://ftp.netcom.com/pub/ka/karl/gd32107.exe  (32 bit version)

Thanks for all the feedback and responses so far. Very encouraging.

Karl Nicholas
Ketchup at cris.com


1.0.007 CHANGES:

1: Added Diff/Consensus Line, Diff/Top Sequence mode to differences

2: Invalidated Consensus lines with asterix when Residues arranged.

3: StrikeOut on Score regions when Residues arranged.

4: Double click score for refresh consistantly.

5: Added no consensus line option.

6: Auto Shade functions update invalidated scores automatically.

7: Insert/Delete Other or Dashes does not effect the score or
consensus lines.

8: Various bugs and gui fixes. One memory lock bug. Additional Error

9: Lots of Help File updates.


GeneDoc's Purpose and Features.

GeneDoc is a full featured Multiple Sequence Format (.MSF) file
alignment editor. GeneDoc is an alignment editor, that is it allows
you to Edit the Alignment
so that different residues from each sequence are lined up with each
other. This is accomplished by moving the residues in one (or all but
one) sequence relative to
the other sequences by inserting or deleting gaps. GeneDoc also
features the exclusive Grab and Drag mode, arranging residues like
beads on a string. The
sequence residues themselves are protected from accidental deletion,
insertion, or modification and cannot be edited. Thus, you can Not
Edit the Sequences.
GeneDoc is also intended to help you bring your genetics research work
to publication with lots of shading, page and font layout features.
This is an editor that
works with the output of the Genetics Computer Groups (GCG) fine suite
of programs for creating Multiple Sequence alignments. 

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
     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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