Abstract
BackgroundThe 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.DescriptionsOrthoClusterDB 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.ConclusionWe have developed an online system for the identification and visualization of synteny blocks among multiple genomes. The system is freely available at .
Highlights
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
The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated genome-wide detection of these functional gene clusters through comparative genome
Most methods developed in the past years for detecting synteny blocks cannot be generally applied because they fail in one or more of the following tasks: (A) comparing multiple genomes; (B) detecting synteny blocks containing interruptions; (C) considering strandedness of genes; and (D) handling one-tomany orthologous relationships
Summary
Accumulating evidence suggests that genes within a genome are not randomly distributed. Most methods developed in the past years for detecting synteny blocks cannot be generally applied because they fail in one or more of the following tasks: (A) comparing multiple genomes; (B) detecting synteny blocks containing interruptions (mismatches); (C) considering strandedness (orientation) of genes; and (D) handling one-tomany orthologous relationships (reviewed in [10]). The View Synteny web page allows users to browse through pre-computed synteny blocks between up to three genomes at the genome, chromosome and gene level. In addition to these two pages, OrthoClusterDB has a Download page, which provides users with the datasets used for generating the pre-computed results and OrthoCluster executables, and a Help page, which includes answers to frequently asked questions, protocols for using Run OrthoCluster and View Synteny pages, and the OrthoCluster tutorial
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