GeneDoc 108: MS/Win program for .msf files

Ketchup Ketchup at cris.com
Sun Mar 17 22:27:13 EST 1996


Please find GeneDoc version 1.0.008 at

http://www.cris.com/~ketchup/genedoc.shtml

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1.0.008 CHANGES:

1: Added Statistic's file generation and Display.

2: Added Score file generation and display.

3: Added Save and Load User Defaults in .INI file functions.

4: Added MFC40.DLL or MFC250.dll in GeneDoc package. Compiled program
to use it.

5: Compensate for Clip area difference between 16 and 32 bit versions,
so can Drag residues to previous and next rows in both versions
properly.

6: Various fixes and changes. 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 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
automatically. 
     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
alignment.

Sequences can easily be added, deleted or reordered within the
alignment.

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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