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ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets

In meiosis, the exchange of DNA between chromosomes by homologous recombination is a critical step that ensures proper chromosome segregation and increases genetic diversity. Products of recombination include reciprocal exchanges, known as crossovers, and non-reciprocal gene conversions or non-cross...

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Autores principales: Anderson, Carol M., Chen, Stacy Y., Dimon, Michelle T., Oke, Ashwini, DeRisi, Joseph L., Fung, Jennifer C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201961/
https://www.ncbi.nlm.nih.gov/pubmed/22046241
http://dx.doi.org/10.1371/journal.pone.0025509
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author Anderson, Carol M.
Chen, Stacy Y.
Dimon, Michelle T.
Oke, Ashwini
DeRisi, Joseph L.
Fung, Jennifer C.
author_facet Anderson, Carol M.
Chen, Stacy Y.
Dimon, Michelle T.
Oke, Ashwini
DeRisi, Joseph L.
Fung, Jennifer C.
author_sort Anderson, Carol M.
collection PubMed
description In meiosis, the exchange of DNA between chromosomes by homologous recombination is a critical step that ensures proper chromosome segregation and increases genetic diversity. Products of recombination include reciprocal exchanges, known as crossovers, and non-reciprocal gene conversions or non-crossovers. The mechanisms underlying meiotic recombination remain elusive, largely because of the difficulty of analyzing large numbers of recombination events by traditional genetic methods. These traditional methods are increasingly being superseded by high-throughput techniques capable of surveying meiotic recombination on a genome-wide basis. Next-generation sequencing or microarray hybridization is used to genotype thousands of polymorphic markers in the progeny of hybrid yeast strains. New computational tools are needed to perform this genotyping and to find and analyze recombination events. We have developed a suite of programs, ReCombine, for using short sequence reads from next-generation sequencing experiments to genotype yeast meiotic progeny. Upon genotyping, the program CrossOver, a component of ReCombine, then detects recombination products and classifies them into categories based on the features found at each location and their distribution among the various chromatids. CrossOver is also capable of analyzing segregation data from microarray experiments or other sources. This package of programs is designed to allow even researchers without computational expertise to use high-throughput, whole-genome methods to study the molecular mechanisms of meiotic recombination.
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spelling pubmed-32019612011-11-01 ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets Anderson, Carol M. Chen, Stacy Y. Dimon, Michelle T. Oke, Ashwini DeRisi, Joseph L. Fung, Jennifer C. PLoS One Research Article In meiosis, the exchange of DNA between chromosomes by homologous recombination is a critical step that ensures proper chromosome segregation and increases genetic diversity. Products of recombination include reciprocal exchanges, known as crossovers, and non-reciprocal gene conversions or non-crossovers. The mechanisms underlying meiotic recombination remain elusive, largely because of the difficulty of analyzing large numbers of recombination events by traditional genetic methods. These traditional methods are increasingly being superseded by high-throughput techniques capable of surveying meiotic recombination on a genome-wide basis. Next-generation sequencing or microarray hybridization is used to genotype thousands of polymorphic markers in the progeny of hybrid yeast strains. New computational tools are needed to perform this genotyping and to find and analyze recombination events. We have developed a suite of programs, ReCombine, for using short sequence reads from next-generation sequencing experiments to genotype yeast meiotic progeny. Upon genotyping, the program CrossOver, a component of ReCombine, then detects recombination products and classifies them into categories based on the features found at each location and their distribution among the various chromatids. CrossOver is also capable of analyzing segregation data from microarray experiments or other sources. This package of programs is designed to allow even researchers without computational expertise to use high-throughput, whole-genome methods to study the molecular mechanisms of meiotic recombination. Public Library of Science 2011-10-25 /pmc/articles/PMC3201961/ /pubmed/22046241 http://dx.doi.org/10.1371/journal.pone.0025509 Text en Anderson et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Anderson, Carol M.
Chen, Stacy Y.
Dimon, Michelle T.
Oke, Ashwini
DeRisi, Joseph L.
Fung, Jennifer C.
ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets
title ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets
title_full ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets
title_fullStr ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets
title_full_unstemmed ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets
title_short ReCombine: A Suite of Programs for Detection and Analysis of Meiotic Recombination in Whole-Genome Datasets
title_sort recombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3201961/
https://www.ncbi.nlm.nih.gov/pubmed/22046241
http://dx.doi.org/10.1371/journal.pone.0025509
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