MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans.

Abstract

Gene duplication occurs via different modes such as segmental and single-gene duplications. Transposed gene duplication, a specific form of single-gene duplication, 'copies' a gene from an ancestral chromosomal location to a novel location. MCScanX is a toolkit for detection and evolutionary analysis of gene colinearity. We have developed MCScanX-transposed, a software package to detect transposed gene duplications that occurred within different epochs, based on execution of MCScanX within and between related genomes. MCScanX-transposed can be also used for integrative analysis of gene duplication modes for a genome and to annotate a gene family of interest with gene duplication modes. MCScanX-transposed is freely available at http://chibba.pgml.uga.edu/mcscan2/transposed/ Supplementary data are available at Bioinformatics online.