Cinteny Server Overview

Cinteny is a flexible and efficient tool for analysis of synteny and evolutionary distances in terms of genome rearrangements (the reversal distance) for multiple genomes. In addition to annotated genomes, which are available for interactive browsing and assessment of synteny and evolutionary distances in terms of orthologous genes, Cinteny can be used with user provided discrete objects, such as sequence tags or other evolutionarily conserved markers. The graphical layer is primarily based on specifically designed library of graphical objects and views, optimized to enable intuitive interpretation of the results.

There are two ways to use the server:

  1. Use the data of pre-loaded genomes
  2. Upload your own data
The same queries may be made in both the modes.

The first feature of the server allows the user to find synteny around a gene of his interest. Next option allows the user to view whole genome synteny map for the genomes chosen. It shows the reversal distance too. A related query option is to find synteny and reversal distance for a chromosome of one genome with a chromosome of another genome more...


Amit U Sinha, Jaroslaw Meller (2007). Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. BMC Bioinformatics, 8:82. (Paper from publisher)

Amit U Sinha, Jaroslaw Meller (2008). Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements. In Proceedings of Pacific Symposium on Biocomputing (PSB): 4-8 January 2008, Hawaii, USA.