Argo Genome Browser

Category Cross-Omics>Sequence Analysis/Tools

Abstract The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes.

This free and open source standalone Java 1.4 application provides:

1) Display of sequence and annotation tracks (from FASTA, Genbank, GFF, BLAST, BED, Wiggle (WIG), and Genscan files).

2) Extensive customization options.

3) Interactive zoom from mega-base to nucleotide resolution.

4) Editing of individual features, supporting manual annotation.

5) Intuitive and elegant comparative perspective (ComBo) (see below...) for viewing dot plots of multiple aligned sequences.

6) Can be run as Java Applet or Webstart application as well as a standalone application.

Though other 'genome browsers' with similar feature sets exist, the manufacturers believe Argo provides a more flexible and intuitive user interface.

Comparative View (ComBo) --

The Comparative View displays sequence alignments. You provide a reference sequence, one or more query sequences, and the alignments for each reference-query pair.

The Comparative View displays the alignments in two (2) ways:

1) 'Perpendicular view' - displays the reference and query sequences on the x and y axes of a dot plot. The glyphs (glyphs are a pictorial form of data collection) on the dot plot represent the alignments.

Multiple query sequences can be displayed on the y axis. This view is best for viewing large sequence regions.

2) 'Parallel view' - displays the reference and query sequences at the top and bottom of a window, with the alignments shown as a stretchy web between them.

Each parallel view shows the reference sequence and one query sequence. This view is best for detailed comparison of smaller segments.

Basic Concepts - Features, Tracks, and Sequence --

The data displayed by Argo is relatively simple: features on sequence.

Simply put, a sequence is a string; a feature is a location on a string.

Features are divided into logical and display groups called "tracks."

"Annotated Transcripts" and "BlastX Hits" are examples of possible tracks.

The main view in Argo, called the "Feature Map," draws features as vertically stacked arrows, with the 'arrow head' indicating the orientation of the feature, and the color indicating the track to which the feature belongs.

Tracks of features may also be segregated into distinct rows.

Here is a Non-biological analogy --

Sequence is like English text, say, the text of Shakespeare's Hamlet; features are like annotations or footnotes that refer to this text.

Imagine you wanted to see the annotations Not merely of one scholar, but of multiple or all scholars at the same time.

Argo would render each scholar's annotations as distinctly colored glyphs (scholar = track, in this analogy).

Overlapping annotations would be stacked vertically. It would quickly become apparent which parts of the play have attracted the most critical attention.

Zooming and clicking would reveal the contents of individual annotations.

Filtering and sorting would remove unwanted clutter. And if you were a scholar, you might use the program to add new annotations with reference to existing ones.

The Argo Genome Browser is open source and provided ‘free of charge’ under the GNU Lesser General Public License (LGPL).

Releases of this software are made about once every two (2) months. The current release, version 1.0.28, was made available for download on 2008-07-07.

Note: Bioinformatics instructors may wish to read about how Argo was used in other courses to illustrate fundamental concepts in computational genomics.

System Requirements

Argo is written in java 1.4.

It has been tested on Windows NT, XP, and Mac OS X, but should run on any operating system that supports java 1.4.


Manufacturer Web Site Argo Genome Browser

Price Free

G6G Abstract Number 20377

G6G Manufacturer Number 101795