SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects
Background High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. Results In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates: 1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D). Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices. 2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats. Conclusions Our experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies.
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Subjects: | F30 - Génétique et amélioration des plantes, C30 - Documentation et information, U30 - Méthodes de recherche, Vitis, bioinformatique, banque de données, polymorphisme génétique, génie génétique, http://aims.fao.org/aos/agrovoc/c_8279, http://aims.fao.org/aos/agrovoc/c_37958, http://aims.fao.org/aos/agrovoc/c_24833, http://aims.fao.org/aos/agrovoc/c_24031, http://aims.fao.org/aos/agrovoc/c_15974, |
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F30 - Génétique et amélioration des plantes C30 - Documentation et information U30 - Méthodes de recherche Vitis bioinformatique banque de données polymorphisme génétique génie génétique http://aims.fao.org/aos/agrovoc/c_8279 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15974 F30 - Génétique et amélioration des plantes C30 - Documentation et information U30 - Méthodes de recherche Vitis bioinformatique banque de données polymorphisme génétique génie génétique http://aims.fao.org/aos/agrovoc/c_8279 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15974 |
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F30 - Génétique et amélioration des plantes C30 - Documentation et information U30 - Méthodes de recherche Vitis bioinformatique banque de données polymorphisme génétique génie génétique http://aims.fao.org/aos/agrovoc/c_8279 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15974 F30 - Génétique et amélioration des plantes C30 - Documentation et information U30 - Méthodes de recherche Vitis bioinformatique banque de données polymorphisme génétique génie génétique http://aims.fao.org/aos/agrovoc/c_8279 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15974 Dereeper, Alexis Nicolas, Stéphane Le Cunff, Loïc Bacilieri, Roberto Doligez, Agnès Péros, Jean-Pierre Ruiz, Manuel This, Patrice SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects |
description |
Background High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. Results In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates: 1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D). Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices. 2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats. Conclusions Our experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies. |
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F30 - Génétique et amélioration des plantes C30 - Documentation et information U30 - Méthodes de recherche Vitis bioinformatique banque de données polymorphisme génétique génie génétique http://aims.fao.org/aos/agrovoc/c_8279 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15974 |
author |
Dereeper, Alexis Nicolas, Stéphane Le Cunff, Loïc Bacilieri, Roberto Doligez, Agnès Péros, Jean-Pierre Ruiz, Manuel This, Patrice |
author_facet |
Dereeper, Alexis Nicolas, Stéphane Le Cunff, Loïc Bacilieri, Roberto Doligez, Agnès Péros, Jean-Pierre Ruiz, Manuel This, Patrice |
author_sort |
Dereeper, Alexis |
title |
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects |
title_short |
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects |
title_full |
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects |
title_fullStr |
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects |
title_full_unstemmed |
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects |
title_sort |
sniplay: a web-based tool for detection, management and analysis of snps. application to grapevine diversity projects |
url |
http://agritrop.cirad.fr/560322/ http://agritrop.cirad.fr/560322/1/document_560322.pdf |
work_keys_str_mv |
AT dereeperalexis sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects AT nicolasstephane sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects AT lecunffloic sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects AT bacilieriroberto sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects AT doligezagnes sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects AT perosjeanpierre sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects AT ruizmanuel sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects AT thispatrice sniplayawebbasedtoolfordetectionmanagementandanalysisofsnpsapplicationtograpevinediversityprojects |
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dig-cirad-fr-5603222024-01-28T19:17:41Z http://agritrop.cirad.fr/560322/ http://agritrop.cirad.fr/560322/ SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. Dereeper Alexis, Nicolas Stéphane, Le Cunff Loïc, Bacilieri Roberto, Doligez Agnès, Péros Jean-Pierre, Ruiz Manuel, This Patrice. 2011. BMC Bioinformatics, 12 (134), 14 p.https://doi.org/10.1186/1471-2105-12-134 <https://doi.org/10.1186/1471-2105-12-134> SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects Dereeper, Alexis Nicolas, Stéphane Le Cunff, Loïc Bacilieri, Roberto Doligez, Agnès Péros, Jean-Pierre Ruiz, Manuel This, Patrice eng 2011 BMC Bioinformatics F30 - Génétique et amélioration des plantes C30 - Documentation et information U30 - Méthodes de recherche Vitis bioinformatique banque de données polymorphisme génétique génie génétique http://aims.fao.org/aos/agrovoc/c_8279 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15974 Background High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow the extensive characterization of Single Nucleotide Polymorphisms (SNPs) and insertion/deletion events (indels) in many plant species. The rapidly increasing amount of re-sequencing and genotyping data generated by large-scale genetic diversity projects requires the development of integrated bioinformatics tools able to efficiently manage, analyze, and combine these genetic data with genome structure and external data. Results In this context, we developed SNiPlay, a flexible, user-friendly and integrative web-based tool dedicated to polymorphism discovery and analysis. It integrates: 1) a pipeline, freely accessible through the internet, combining existing softwares with new tools to detect SNPs and to compute different types of statistical indices and graphical layouts for SNP data. From standard sequence alignments, genotyping data or Sanger sequencing traces given as input, SNiPlay detects SNPs and indels events and outputs submission files for the design of Illumina's SNP chips. Subsequently, it sends sequences and genotyping data into a series of modules in charge of various processes: physical mapping to a reference genome, annotation (genomic position, intron/exon location, synonymous/non-synonymous substitutions), SNP frequency determination in user-defined groups, haplotype reconstruction and network, linkage disequilibrium evaluation, and diversity analysis (Pi, Watterson's Theta, Tajima's D). Furthermore, the pipeline allows the use of external data (such as phenotype, geographic origin, taxa, stratification) to define groups and compare statistical indices. 2) a database storing polymorphisms, genotyping data and grapevine sequences released by public and private projects. It allows the user to retrieve SNPs using various filters (such as genomic position, missing data, polymorphism type, allele frequency), to compare SNP patterns between populations, and to export genotyping data or sequences in various formats. Conclusions Our experiments on grapevine genetic projects showed that SNiPlay allows geneticists to rapidly obtain advanced results in several key research areas of plant genetic diversity. Both the management and treatment of large amounts of SNP data are rendered considerably easier for end-users through automation and integration. Current developments are taking into account new advances in high-throughput technologies. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/560322/1/document_560322.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/1471-2105-12-134 10.1186/1471-2105-12-134 info:eu-repo/semantics/altIdentifier/doi/10.1186/1471-2105-12-134 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/1471-2105-12-134 |