SPoRE

SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis

 

Overview:

Meiotic recombination between homologous chromosomes provides natural combinations of genetic variations and is a main driving force of evolution. It is initiated via programmed DNA double-strand breaks (DSB) and involves a specific axial chromosomal structure. So far, recombination regions have been mainly determined by experiments, both expensive and time-consuming.

SPoRE is a mathematical model that describes the non-uniform localization of DSB and axis proteins sites, and distinguishes high versus low protein density. It is based on a combination of genomic signals whose contribution is precisely quantified. It models axis proteins accumulation in gene end positions with a discrete approximation of their diffusion and convection along genes. It models DSB accumulation in gene promoter positions with intergenic region length and GC-content. It can be used for prediction.

SPoRE is parameterized in an obvious way and it is easy to understand from a biological viewpoint. In particular, SPoRE model is consistent with what is known from wet-lab experiments. When compared to Saccharomyces cerevisiae experimental data, SPoRE predicts axis protein and DSB positions with high sensitivity and precision, axis protein density with an average local correlation r=0.63 and DSB density with an average local correlation r=0.62. SPoRE outbreaks previous DSB predictors, which are based on nucleotide patterning, and it reaches 85% of success rate in DSB prediction compared to 54% obtained by available tools on a benchmarked dataset.

Download

The SPoRE package can be downloaded here.

The SPoRE documentation can be downloaded here.

SPoRE models for axis proteins on 4 yeast species, in wig format, are downloadable here.

SPoRE models for DSBs on 4 yeast species, in wig format, are downloadable here.

Benchmark datasets for SPoRE evaluation against existing predictive tools (text files), are downloadable here.

Previously published S.cerevisiae experimental curves for axis proteins and DSB distribution, in wig format, are downloadable here.

Licence:

The SPoRE program has been developed under the CeCILL licence.

 

Contacts:

For questions, comments, or suggestions feel free to contact Raphael Champeimont or Alessandra Carbone.

Reference:

If you are using SPoRE, please cite:

Raphaël Champeimont, Alessandra Carbone, SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis, BMC Bioinformatics, 2014.

Last Update Sept. 2013