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EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

(2016) NUCLEIC ACIDS RESEARCH. 44(W1). p.W142-W146
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/.
Keywords
GENOME, IDENTIFICATION, YEAST, SEQUENCING REVEALS, GENETIC SCREENS, MUTMAP

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Citation

Please use this url to cite or link to this publication:

Chicago
Pulido Tamayo, Sergio, Jorge Duitama, and Kathleen Marchal. 2016. “EXPLoRA-web: Linkage Analysis of Quantitative Trait Loci Using Bulk Segregant Analysis.” Nucleic Acids Research 44 (W1): W142–W146.
APA
Pulido Tamayo, S., Duitama, J., & Marchal, K. (2016). EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. NUCLEIC ACIDS RESEARCH, 44(W1), W142–W146.
Vancouver
1.
Pulido Tamayo S, Duitama J, Marchal K. EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis. NUCLEIC ACIDS RESEARCH. 2016;44(W1):W142–W146.
MLA
Pulido Tamayo, Sergio, Jorge Duitama, and Kathleen Marchal. “EXPLoRA-web: Linkage Analysis of Quantitative Trait Loci Using Bulk Segregant Analysis.” NUCLEIC ACIDS RESEARCH 44.W1 (2016): W142–W146. Print.
@article{7206896,
  abstract     = {Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/.},
  author       = {Pulido Tamayo, Sergio and Duitama, Jorge and Marchal, Kathleen},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {GENOME,IDENTIFICATION,YEAST,SEQUENCING REVEALS,GENETIC SCREENS,MUTMAP},
  language     = {eng},
  number       = {W1},
  pages        = {W142--W146},
  title        = {EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis},
  url          = {http://dx.doi.org/10.1093/nar/gkw298},
  volume       = {44},
  year         = {2016},
}

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