Integrated Genome Browser (IGB)

Category Cross-Omics>Sequence Analysis/Tools and Cross-Omics>Next Generation Sequence Analysis/Tools

Abstract The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself.

IGB is implemented using the Java programming language and should be able to run on almost any computer.

IGB Development history --

IGB is an open source, publicly-funded project, but it did Not start out that way. Initial development of the software was largely funded by Affymetrix, Inc., which donated the IGB software to the community in 2005.

Since then, community developers have continued to contribute their time and efforts to improving the software.

IGB is the flagship product of the 'open source' Genoviz project, which aims to develop visualization software for bioinformatics and genomics.

IGB is based on a library of visualization "widgets" called the Genoviz toolkit, the newest version of the Neomorphic Genome Software Developers Kit.

Neomorphic was a bioinformatics software company started by graduate students from the Berkeley Drosophila Genome Project back in the late 1990s.

In early 2000, Affymetrix purchased Neomorphic. In 2005, Affymetrix released the Genoviz toolkit and IGB as open source, free software.

You can use IGB to --

1) View Expressed Sequence Tag (EST)/complementary DNA (cDNA) alignment results -

Next-generation sequencing technologies are making it much easier for individual labs to produce huge volumes of short- and long-read sequencing data.

To get maximum value from these data, you often need to view the sequence reads alongside all the other known features in a genome.

Using tools like the BLAST-Like Alignment Tool (BLAT) - (BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments); and

sim4 (sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene); you can align your reads against the genome and then use IGB to view the alignments alongside canonical 'gene models' provided by organizations such as The Arabidopsis Information Resource (TAIR) - (TAIR maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana).

IGB can read data in a variety of different formats, including: psl (from BLAT), bed [UCSC Genome Bioinformatics - (see G6G Abstract Number 20197)], and Fasta (for sequence files).

2) View gene models and other annotations data -

IGB can load data via the Internet using Web services (and from local files and directories).

Currently, IGB accesses data provided by two (2) different sites - the manufacturers 'BioViz ArabiDAS' site, which serves Arabidopsis data, and another site hosted by Affymetrix (NetAffx) which serves data from the human and many other genomes.

Ultimately, the manufacturer plans to support other plant genomes, as well.

Note: Data sites interested in hosting their own IGB-compatible data server sites should contact the manufacturer for details.

3) Explore tiling array data -

IGB can load data from tiling array results as genome graphs, which display probe intensity data alongside the genomic sequence.

IGB can display positional, numerical data in the form of graphs, where the x-axis is the sequence and the y-axis represents numerical data, like probe intensity values.

IGB version 6.0 is released to Source Forge --

New features are listed below -

IGB Client features:

1) Compiled with Java 6;

2) Enhanced data source preferences page;

3) Unification of "Pattern Search", "Name Search", and "Annotation Browser" tabs;

4) Auto-loading of features (if specified by DAS/2 server);

5) Data provider hyperlinks and icons;

6) Feature hyperlinks and description tooltips;

7) QuickLoad annots.xml file (similar to DAS/2);

8) GFF and BED parsing bug fixes;

9) Warnings for chromosome conflicts; and

10) Assorted graphical user interface (GUI) enhancements and bug fixes.

Distributed Annotation System (DAS)/2 (see G6G Abstract Number 20488).

Server features:

1) File indexing - reduces memory requirements by up to 90%, often reducing startup time as well.

2) Improved ID searches - reduces network traffic, thus speeding up client-side search.

3) Warnings for chromosome conflicts; and

4) Additional annots.xml properties.

System Requirements

Contact manufacturer.

Manufacturer

Manufacturer Web Site Integrated Genome Browser (IGB)

Price Contact manufacturer.

G6G Abstract Number 20489

G6G Manufacturer Number 104112