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SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis
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 regi...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268827/ https://www.ncbi.nlm.nih.gov/pubmed/25495332 http://dx.doi.org/10.1186/s12859-014-0391-1 |
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author | Champeimont, Raphaël Carbone, Alessandra |
author_facet | Champeimont, Raphaël Carbone, Alessandra |
author_sort | Champeimont, Raphaël |
collection | PubMed |
description | 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0391-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4268827 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-42688272014-12-17 SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis Champeimont, Raphaël Carbone, Alessandra BMC Bioinformatics Methodology Article 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/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0391-1) contains supplementary material, which is available to authorized users. BioMed Central 2014-12-11 /pmc/articles/PMC4268827/ /pubmed/25495332 http://dx.doi.org/10.1186/s12859-014-0391-1 Text en © Champeimont and Carbone; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Champeimont, Raphaël Carbone, Alessandra SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis |
title | SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis |
title_full | SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis |
title_fullStr | SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis |
title_full_unstemmed | SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis |
title_short | SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis |
title_sort | spore: a mathematical model to predict double strand breaks and axis protein sites in meiosis |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268827/ https://www.ncbi.nlm.nih.gov/pubmed/25495332 http://dx.doi.org/10.1186/s12859-014-0391-1 |
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