Similar softwares
Multiple Collinearity Scan - mcscan
MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.
Availability
Current version: 0.8 (released Nov. 2008) (also available on GITHUB)
Disclaimer: this software is free to use, modify, redistribute without any restrictions.
Installation: unpack the tarball and type "make" (Currently Linux and Cygwin platform are supported).
Documentation: Read online for a quick start, or PDF manual.
Results
The MCscan algorithm has been tested in several taxonomic groups, including:
- Yeast
- Paramecium
- Fugu
- Plants
Results and procedures for plant species can be accessed here.
Reference
- Tang, H., Bowers, J.E., Wang, X., Ming, R., Alam, M., and Paterson, A.H. (2008) Synteny and Collinearity in Plant Genomes, Science, 320, 486-488. [ Online ]
- Tang, H., Wang, X., Bowers, J.E., Ming, R., Alam, M., and Paterson, A.H. (2008) Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps, Genome Research, 18, 1944-1954. [ Online ] [ Supplements ]
- Tang, H., Bowers, J.E., Wang, X., and Paterson, A.H. (2009) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage, PNAS. [ Online ] [ Supplements ]
Contact
All bug reports, suggestions or questions are very welcome and should be dumped to
Haibao Tang : bao at uga dot edu |