Main
The synteny information is computed from the correspondence between proteins of different organisms (Bi-Directional Best Hits – BDBH) and the conserved order of the corresponding genes along the genomes..
In addition to the local view described above, four connected global views are available: Dotplot, Lineplot, Phylogenetic profile and Gene List. All these views permit to go back to the local view.
Local View
Synteny is presented in a local genomic area
A color is randomly assigned to every gene of the reference organism. By construction, BDBH genes get the same color as the reference gene and orphan genes remain black. When the user clicks on a gene to show its local synteny, the other genomes shift to be aligned with the main sequence and the non-syntenic genes fade away.
Lineplot
The Line Plot shows the organization of syntenic groups at the chromosome level.
Dotplot
The Dot Plot shows the synteny ruptures and the chromosome re-arrangements.
The user can select graphically a part of the BDBH to export in a flat files.
Phylogenetic profile
The phylogenetic profile consists in a map of BLASTP hits sorted according to a phylogenetic tree.
In the left side, the interface allows to browse the entire genome to see the hit map of BLASTP hits. The geometry of the cell present the difference of the gene size. Each cell can be clicked to go to the local view. The phylogenetic tree can reorder the hitmap column. In right side a global map present the entire hitmap pattern. This representation allows to show gene conversation (or loose) by phylogenetic group of organisms.
Circular View
iIn contrast to the central local view, where absolute coordinates of aligned genomes do not coincide, this global circular view indicates whether the conserved syntenic region is localised identically in complete genomes. Several kinds of circular representations are available, where the outer circle colours represent either sequence similarity heat maps or genome categories
