BACKGROUND: The recent availability of an expanding collection of genome 
sequences driven by technological advances has facilitated comparative genomics 
and in particular the identification of synteny among multiple genomes. However, 
the development of effective and easy-to-use methods for identifying such 
conserved gene clusters among multiple genomes-synteny blocks-as well as 
databases, which host synteny blocks from various groups of species (especially 
eukaryotes) and also allow users to run synteny-identification programs, lags 
behind.
DESCRIPTIONS: OrthoClusterDB is a new online platform for the identification and 
visualization of synteny blocks. OrthoClusterDB consists of two key web pages: 
Run OrthoCluster and View Synteny. The Run OrthoCluster page serves as web 
front-end to OrthoCluster, a recently developed program for synteny block 
detection. Run OrthoCluster offers full control over the functionalities of 
OrthoCluster, such as specifying synteny block size, considering order and 
strandedness of genes within synteny blocks, including or excluding nested 
synteny blocks, handling one-to-many orthologous relationships, and comparing 
multiple genomes. In contrast, the View Synteny page gives access to perfect and 
imperfect synteny blocks precomputed for a large number of genomes, without the 
need for users to retrieve and format input data. Additionally, genes are 
cross-linked with public databases for effective browsing. For both Run 
OrthoCluster and View Synteny, identified synteny blocks can be browsed at the 
whole genome, chromosome, and individual gene level. OrthoClusterDB is freely 
accessible.
CONCLUSION: We have developed an online system for the identification and 
visualization of synteny blocks among multiple genomes. The system is freely 
available at (http://genome.sfu.ca/orthoclusterdb/).