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GeneDoc 2.0.1 Multiple Sequence and Alignment Editor
GeneDoc's Purpose and Features.
GeneDoc is a full featured Multiple Sequence Alignment Editor and Shading Utility. GeneDoc is also intended to help you bring your genetics research work to publication with lots of shading, page and font layout features. GeneDoc reads either .MSF Multiple Sequence alignment files or can import FASTA format files to be saved as a .MSF file project. GeneDoc is an alignment editor, meaning that 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. A residue editing mode is available to allow you to change the residues values themselves. Built in DayHoff and BlockSum scoring functions allow you to be sure your alignment changes are improving the score. Scores can be determined either by a sum of pairs method or with the phylogenetic tree support.
GeneDoc also provides a comprehensive range of display shading modes, functions and capabilities. Outlined below, these functions give flexible ways to look at the data and to show important concepts.
GeneDoc provides output in several ways. You can print directly to the printer, export BitMaps, Text, MetaFiles or MAC style Pict files.
In addition to extensive display and highlighting features GeneDoc also has a growing list of analytical features. These analytical features are intended to help you learn as much as possible about the sequences you are studying from the alignment. These features include two different methods for scoring the alignment, summary statistics describing the relatedness of the sequences, the ability to compare and contrast groups of sequences within the alignment, and the ability to superimpose three dimensional structural information on either individual sequences or groups of sequences when the structure of a sequence is known. Where possible these analytical features make use of GeneDoc's display features to help you visualise the analytical results.
GeneDoc's features
Five 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.
- Properties mode focuses attention on residues that have maintained a specific chemical or physical property throughout the evolution of the molecule even though the specific residue varies.
- Structure mode allows you to highlight different secondary structure elements when one (or more) of the sequences has a known three dimensional structure.
GeneDoc supports dividing the sequences into distinct groups. This is very useful for alignments of protein superfamilies where each family can be treated as a different group. Each group can be highlighted separately to help you explore differences between the groups as well as their common features. This helps direct attention to sequence features associated with the differences in biochemistry among the groups.
Scoring functions allows quantitative evaluation of whether alignment changes are improving or degrading the alignment.
Score with either sum of pairs or with phylogenetic trees.
Phylogenetic tree scoring uses the weighted maximum parsimony algorithm first described by D. D. Sankoff. This is particularly useful in deciding on the best placement of several gaps in a small region of the alignment.
Sum of pairs scoring and most currently used multiple sequence alignment programs have a strong tendency to force gaps into the same locations in the sequences of an alignment even when the gaps were clearly the result of different insertion or deletion events in the evolutionary history of the sequences. GeneDoc allows you to investigate and correct for this.
Import phylogenetic trees in either Phylip or Nexus formats, or build your own with GeneDoc's GUI interface.
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.
The statistics function summarizes the similarity and divergence among the pairs of sequences.
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 as BitMaps, Text Files or Pict Files.
Residue editing mode for easy modification of data.
Availability
GeneDoc is available free of charge for the following versions of Microsoft Windows: Windows 3.x, Windows/95 and Windows/NT. There is also a version for a DEC Alpha running Windows/NT.
Written by: Karl Nicholas
Resources and further information:
GeneDoc Home page
http://www.cris.com/~ketchup/genedoc.shtml
Download instructions for the GeneDoc program (all versions)
http://www.cris.com/~ketchup/gddl.htm
Contact: Karl Nicholas, e-mail: ketchup@cris.com
Genetics Computer Group (GCG)
http://www.gcg.com/
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