MareyMap: an R-based tool with graphical interface for estimating recombination rates

UNLABELLED Comparing genetic and physical maps (the so-called Marey map approach) is still the most widely used approach to estimate genome-wide recombination rates. Remarkably, there is no available bioinformatics tool specifically devoted to Marey map approach. Here, we developed such a tool called MareyMap based on GNU R and Tcl/Tk. MareyMap offers a user-friendly graphical interface and includes useful features, such as data cleaning process, sophisticated interpolation methods to estimate local rates, possibility of complex queries, various range of import-export files. Moreover, MareyMap comes with ready-to-use maps for human, Drosophila, Caenorhabditis elegans and Arabidopsis. MareyMap has been made so that it can be easily upgraded with new data and interpolation methods. AVAILABILITY http://pbil.univ-lyon1.fr/software/mareymap/.

[1]  B. Charlesworth,et al.  Steps in the evolution of heteromorphic sex chromosomes , 2005, Heredity.

[2]  J. Dvorak,et al.  Recombination: an underappreciated factor in the evolution of plant genomes , 2007, Nature Reviews Genetics.

[3]  Brian Charlesworth,et al.  On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. , 2002, Molecular biology and evolution.

[4]  Laurence D. Hurst,et al.  Evidence for co-evolution of gene order and recombination rate , 2003, Nature Genetics.

[5]  Steffen Möller,et al.  Non-linear conversion between genetic and physical chromosomal distances , 2004, German Conference on Bioinformatics.

[6]  L. Duret,et al.  Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[7]  P. Donnelly,et al.  Estimating recombination rates from population genetic data. , 2001, Genetics.

[8]  Kenneth Lange,et al.  Spline Methods for the Comparison of Physical and Genetic Maps , 2003, J. Comput. Biol..

[9]  D. Gudbjartsson,et al.  A high-resolution recombination map of the human genome , 2002, Nature Genetics.

[10]  D. Presgraves,et al.  Recombination Enhances Protein Adaptation in Drosophila melanogaster , 2005, Current Biology.

[11]  S. Wright,et al.  Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. , 2003, Genome research.

[12]  A. Chakravarti.  A graphical representation of genetic and physical maps: the Marey map. , 1991, Genomics.

[13]  P. Deloukas,et al.  Comparison of human genetic and sequence-based physical maps , 2001, Nature.

[14]  P. Donnelly,et al.  A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome , 2005, Science.

[15]  A. Clark,et al.  Genetic recombination: Intron size and natural selection , 1999, Nature.