Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of particular interest in the reconstruction and biotechnological manipulation of metabolic pathways. Over the last years, the OmnilogTM Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of URLanisms. However, software that could directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype correlation is still missing. Here we present DuctApe, a suite that allows the analysis of both genomic sequences and PM data, to find any metabolic difference among PM experiments and to correlate them with KEGG pathways and gene presence/absence patterns. As example, an application of the program to four Sinorhizobium meliloti strains is also presented. The source code and tutorials are available at URL
Addressing the functionality of genomes is one of the most important and challenging tasks of today's biology. In particular the ability to link genotypes to corresponding phenotypes is of interest in the reconstruction and biotechnological manipulation of metabolic pathways. Over the last years, the OmniLogTM Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of URLanisms. However, computational tools that could directly link PM data with the gene(s) of interest followed by the extraction of information on genephenotype correlation are still missing. Here we present DuctApe, a suite that allows the analysis of both genomic sequences and PM data, to find metabolic differences among PM experiments and to correlate them with KEGG pathways and gene presence/absence patterns. As example, an application of the program to four bacterial datasets is presented. The source code and tutorials are available at URL
D
particular
R
OmnilogTM
OmniLogTM
R
software
computational tools
R
gene-phenotype correlation is
genephenotype correlation are
R
any metabolic difference
metabolic differences
R
Sinorhizobium meliloti strains is also
bacterial datasets is