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OrthoClusterDB: an online platform for synteny blocks
Man-Ping Ng1, Ismael A Vergara, Christian Frech
1Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada. pennyng119@gmail.com
BMC Bioinformatics
|June 25, 2009
Summary
OrthoClusterDB is a new online platform for identifying and visualizing synteny blocks across multiple genomes. This tool aids comparative genomics research by providing easy access to conserved gene clusters and precomputed synteny data.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Advancements in genome sequencing have spurred comparative genomics.
- Identifying conserved gene clusters (synteny blocks) across multiple genomes is crucial but challenging.
- Existing databases and tools for synteny block analysis are limited.
Purpose of the Study:
- To develop an accessible online platform for identifying and visualizing synteny blocks.
- To provide a user-friendly interface for comparative genomics analysis.
- To host precomputed synteny data for a wide range of species.
Main Methods:
- Developed OrthoClusterDB, an online platform with two main components: Run OrthoCluster and View Synteny.
- Run OrthoCluster provides a web front-end to the OrthoCluster program for customizable synteny block detection.
- View Synteny offers access to precomputed synteny blocks and cross-links genes to public databases.
Main Results:
- OrthoClusterDB enables the identification and visualization of synteny blocks at various levels (genome, chromosome, gene).
- The platform supports detailed analysis, including gene order, strandedness, and nested blocks.
- Users can compare multiple genomes and handle complex orthologous relationships.
Conclusions:
- OrthoClusterDB is a freely accessible online system for synteny block identification and visualization.
- The platform facilitates comparative genomics by simplifying the analysis of conserved gene clusters.
- OrthoClusterDB is available at http://genome.sfu.ca/orthoclusterdb/.
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