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CDROM: Classification of Duplicate gene RetentiOn Mechanisms
- Source :
- BMC Evolutionary Biology
- Publication Year :
- 2016
- Publisher :
- BioMed Central, 2016.
-
Abstract
- Gene duplication is a major source of new genes that is thought to play an important role in phenotypic innovation. Though several mechanisms have been hypothesized to drive the functional evolution and long-term retention of duplicate genes, there are currently no software tools for assessing their genome-wide contributions. Thus, the evolutionary mechanisms by which duplicate genes acquire novel functions remain unclear in a number of taxa. In a recent study, researchers developed a phylogenetic approach that uses gene expression data from two species to classify the mechanisms underlying the retention of duplicate genes (Proc Natl Acad Sci USA 110:1740917414, 2013). We have implemented their classification method, as well as a more generalized method, in the R package CDROM, enabling users to apply these methods to their data and gain insights into the origin of novel biological functions after gene duplication. The CDROM R package, source code, and user manual for the R package are available for download from CRAN at https://cran.rstudio.com/web/packages/CDROM/ . Additionally, the CDROM R source code, user manual for running CDROM from the source code, and sample dataset used in this manuscript can be accessed at www.personal.psu.edu/rua15/software.html . CDROM is the first software package that enables genome-wide classification of the mechanisms driving the long-term retention of duplicate genes. It is user-friendly and flexible, providing researchers with a tool for studying the functional evolution of duplicate genes in a variety of taxa.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Source code
Gene duplication
Neofunctionalization
media_common.quotation_subject
Biology
010603 evolutionary biology
01 natural sciences
Evolution, Molecular
03 medical and health sciences
Functional evolution
Software
Genes, Duplicate
Subfunctionalization
Animals
Humans
Gene
Ecology, Evolution, Behavior and Systematics
Phylogeny
media_common
Information retrieval
business.industry
R package
030104 developmental biology
ComputingMethodologies_PATTERNRECOGNITION
CD-ROM
Evolutionary biology
Gene expression evolution
business
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 14712148
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- BMC Evolutionary Biology
- Accession number :
- edsair.doi.dedup.....494af48d4e04ea28502451554380b762