EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis.
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/.
Department of Information Technology, iGent Toren, Technologiepark 15, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Gent, Belgium Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium.
Sergio
S
Pulido-Tamayo
Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), 763537 Cali, Colombia.
Jorge
J
Duitama
Department of Information Technology, iGent Toren, Technologiepark 15, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, UGent, Technologiepark 927, 9052 Gent, Belgium Bioinformatics Institute Ghent, Technologiepark 927, 9052 Gent, Belgium Department of Genetics, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa kathleen.marchal@intec.ugent.be.
Kathleen
K
Marchal
D000465:Algorithms; D000483:Alleles; D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D003196:Computer Graphics; D005787:Gene Frequency; D059014:High-Throughput Nucleotide Sequencing; D016247:Information Storage and Retrieval; D020407:Internet; D015810:Linkage Disequilibrium; D010641:Phenotype; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D012984:Software