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

Sergio Pulido Tamayo, Jorge Duitama and Kathleen Marchal UGent (2016) NUCLEIC ACIDS RESEARCH. 44(W1). p.W142-W146
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/.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
GENOME, IDENTIFICATION, YEAST, SEQUENCING REVEALS, GENETIC SCREENS, MUTMAP
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
44
issue
W1
pages
W142 - W146
Web of Science type
Article
Web of Science id
000379786800024
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
10.162 (2016)
JCR rank
14/286 (2016)
JCR quartile
1 (2016)
ISSN
0305-1048
DOI
10.1093/nar/gkw298
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
7206896
handle
http://hdl.handle.net/1854/LU-7206896
date created
2016-05-11 15:42:49
date last changed
2017-04-27 08:41:08
@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},
}

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.