MSDino: Ks-Based Tool for Detection of Micro-Synteny

ynteny is the conserved block within chromosomes. With synteny, researchers can delineate the history of genome conformation such as genome duplication or triplication and speciation. MCScan and PGDD (Plant Genome Duplication Database) are representative synteny detecting tool and database based on synteny, respectively. However, there are not currently favorable methods to identify the micro-synteny, the small-scale syntenic block including two or more genes. Because, it is difficult to confirm whether potential micro-syntenic block was caused by genome duplication, tandem repeat or coincidental enumeration genes. So, we introduce MSDino (Micro-syntenic detection tool) to detect micro-synteny block using two genes with two factors. First, the distance between two genes should be close enough to give evidence that they move together in evolution. Second, the Ks value of each gene has to be similar, or they are not originated at the same time. Additionally, comparison between Ks value of each gene pair in synteny and Ks distribution of whole genome enables to infer the originated time of the micro-syntenic block relative to speciation or genome duplication.