Blast Atlas

Contents

• Project overview
• Publications
• Availability

Project Overview

Blast Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, Blast Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Figure 1: A three-dimensional map showing the bacterial COG dataset. The COG dataset provides a functional backdrop for analysis and comparison of genome-scale protein or gene collections.

Figure 2: The COG dataset, rendered in two dimensions.

Blast Atlas extends earlier work on SilverMap in several important ways. While there remains a shared theme centered on the use of maplike interfaces to allow users to manage, navigate and comprehend large similarity-based comparative genomics datasets, Blast Atlas introduces a global organisational principle based on gene function. Where SilverMap operates on a gene-by-gene level, Blast Atlas exploits the function-based frame of reference to permit analysis and comparison between genome-scale gene collections.

The system provides a choice between an immersive three-dimensional viewing experience (Figure 1) or a more traditional two-dimensional display (Figure 2) that is more appropriate for the production of printed graphical material. The graphical display is augmented by synchronised property tables that allow the user to filter the collection, view and edit gene annotations and link out to external data sources via NCBI Entrez and Bio2RDF.

Blast Atlas uses the COG dataset – Clustors of Orthologous Groups, hosted by NCBI at http://www.ncbi.nlm.nih.gov/COG/ – to provide biological context and organising structure against which genes from multiple input collections may be superimposed. This gives immediate support for gene functional classification, where previously uncharacterised genes are assigned a putative biological function based on similarity to reference sequences from the COG dataset. In addition to sequence similarity, the tool provides detailed alignment views and access to relevant external information via the linked external resources. With the ability to load and manipulate logical combinatuions of genes from multiple source genomes, a user may compare and contrast the genetic content of two or more genomes, yielding a function-based genome comparison system that complements more traditional position-based genome comparison tools.

Publications

• Buckingham, L., Hogan, J., Mann, S., Wirges, S., "Blast Atlas: a function based multiple genome browser", Microsoft eScience Workshop 2010, Berkely CA, 10-13 October 2010.

• Buckingham, L., Hogan, J., "Blast Atlas: a virtual observatory for genomes". In: HPC for Life Sciences workshop at the sixth IEEE e-Science conference, Brisbane, Australia, 6-11 December 2010.

Availability

Blast Atlas is an open source product released under the Microsoft Public License. Source and binary versions of the protoype implementation are scheduled for release in early December 2010 at http://qutbio.codeplex.com.