title: SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  SPoRE is a mathematical model that describes the non-uniform localisation of DSB and axis proteins sites, and distinguishes high versus low protein density. It is based on a combination of genomic signals, based on what is known from wet-lab experiments, whose contribution is precisely quantified. It models axis proteins accumulation at gene 5'-ends with a discrete approximation of their diffusion and convection along genes. It models DSB accumulation at approximated gene promoter positions with intergenic region length and GC-content. SPoRE can be used for prediction and it is parameterised in an obvious way that makes it easy to understand from a biological viewpoint.
  
  
  CONCLUSIONS
  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.SPoRE is available at the address http://www.lcqb.upmc.fr/SPoRE/.
authors.forename: Raphaël
authors.initials: R
authors.lastname: Champeimont
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris F-75006, France. Alessandra.Carbone@lip6.fr.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Carbone
mesh_terms: D001482:Base Composition; D002875:Chromosomes; D053903:DNA Breaks, Double-Stranded; D023281:Genomics; D008540:Meiosis; D008954:Models, Biological; D011995:Recombination, Genetic; D012441:Saccharomyces cerevisiae / Q000166:cytology* / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis* / Q000378:metabolism; D015003:Yeasts / Q000166:cytology / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins