BioMercator: integrating genetic maps and QTL towards discovery of candidate genes

Breeding programs face the challenge of integrating information from genomics and from quantitative trait loci (QTL) analysis in order to identify genomic sequences controlling the variation of important traits. Despite the development of integrative databases, building a consensus map of genes, QTL...

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Bibliographic Details
Published in:Bioinformatics 2004-09, Vol.20 (14), p.2324-2326
Main Authors: Arcade, Anne, Labourdette, Aymeric, Falque, Matthieu, Mangin, Brigitte, Chardon, Fabien, Charcosset, Alain, Joets, Johann
Format: Article
Language:English
Subjects:
Algorithms
Biological and medical sciences
Chromosome Mapping - methods
Computer Graphics
Computer Science
Consensus Sequence
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Quantitative Trait Loci - genetics
Sequence Alignment - methods
Sequence Analysis, DNA - methods
Software
Systems Integration
User-Computer Interface
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Summary:Breeding programs face the challenge of integrating information from genomics and from quantitative trait loci (QTL) analysis in order to identify genomic sequences controlling the variation of important traits. Despite the development of integrative databases, building a consensus map of genes, QTL and other loci gathered from multiple maps remains a manual and tedious task. Nevertheless, this is a critical step to reveal co-locations between genes and QTL. Another important matter is to determine whether QTL linked to same traits or related ones is detected in independent experiments and located in the same region, and represents a single locus or not. Statistical tools such as meta-analysis can be used to answer this question. BioMercator has been developed to automate map compilation and QTL meta-analysis, and to visualize co-locations between genes and QTL through a graphical interface. Availability: Available upon request (http://moulon/~bioinfo/BioMercator/). Free of charge for academic use.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bth230