SUMMARY: Compilation of genetic maps combined to quantitative trait loci (QTL) meta-analysis has proven to be a powerful approach contributing to the identification of candidate genes underlying quantitative traits. BioMercator was the first software offering a complete set of algorithms and visualization tool covering all steps required to perform QTL meta-analysis. Despite several limitations, the software is still widely used. We developed a new version proposing additional up to date methods and improving graphical representation and exploration of large datasets. AVAILABILITY AND IMPLEMENTATION: BioMercator V3 is implemented in JAVA and freely available (http://moulon.inra.fr/biomercator) CONTACT: [email protected].

MOTIVATION: A large part of the maize B73 genome sequence is now available and emerging sequencing technologies will offer cheap and easy ways to sequence areas of interest from many other maize genotypes. One of the steps required to turn these sequences into valuable information is gene content prediction. To date, there is no publicly available gene predictor specifically trained for maize sequences. To this end, we have chosen to train the EuGène software that can combine several sources of evidence into a consolidated gene model prediction. AVAILABILITY: http://genome.jouy.inra.fr/eugene/cgi-bin/eugene_form.pl.

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.