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

Bioinformatics. 2013 Jun 1;29(11):1458-60. doi: 10.1093/bioinformatics/btt150. Epub 2013 Mar 28.


Summary: 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.

Availability: MCScanX-transposed is freely available at

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Evolution, Molecular
  • Gene Duplication*
  • Genomics
  • Software*