SynteView

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SynteView allows a fast and easy visualization of conservation of gene adjacency in many prokaryotic genomes for which orthology and neighbourhood data have been computed and stored in SynteBase, a dedicated relational database. It has been developed by Frédéric Lemoine, a PhD student working at the Institut de Genetique et Microbiologie and the Laboratoire de Recherche en Informatique at the University Paris-Sud XI.

SynteView displays synteny comparison between a reference genome (choosen by the user) and a set of genomes choosen among a total of 600 prokaryotic genomes stored in SynteBase.

In the example below (Screenshot) the reference genome Escherichia coli is displayed on the first line of the window (blue background). Each gene is symbolized by a rectangle harbouring the corresponding name and coloured according its strand location: + (blue) or - (yellow).

Next lines display the synteny blocks detected in the compared genomes that are sorted by their taxonomic proximity to the reference genome. The orthologous genes belonging to a synteny block are shown by rectangles with the same colour code. Clicking on a rectangle allows displaying information about the corresponding gene on the left panel such as its GenBank PID, its name, the species and the replicon to which it belongs, the function of its product, and its exact location on the chromosome. This information panel contains also a text field allowing making simple queries such as searching a protein function or a gene name or PID in the reference genome, as well as searching synteny blocks that contains more than x genes.

The bottom lines show the rate of conservation of each syntenic gene in the compared genomes as a histogram (in blue).

SynteView is available as a Java Web Start application, making it easy to run.

More tools and detailed instructions are available in the Documents part.

Screenshot

Publication

Lemoine, F.; Labedan, B. & Lespinet, O. SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. BMC Bioinformatics, 2008, 9, 536
 
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