title: DuctApe: a suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data.
abstract: 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 OmniLog™ Phenotype Microarray (PM) technology has been used to address many specific issues related to the metabolic functionality of microorganisms. However, computational tools that could directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype 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 http://combogenomics.github.io/DuctApe/.
authors: Department of Biology, University of Florence, Florence, Italy. Electronic address: marco.galardini@unifi.it.
authors: Marco
authors: M
authors: Galardini
authors: Department of Biology, University of Florence, Florence, Italy.
authors: Alessio
authors: A
authors: Mengoni
authors: Interdisciplinary Research Institute USR3078, CNRS-Université Lille Nord de France, Villeneuve d'Ascq, France.
authors: Emanuele G
authors: EG
authors: Biondi
authors: Department of Biology, University of Florence, Florence, Italy.
authors: Roberto
authors: R
authors: Semeraro
authors: Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per lo studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Rome, Italy.
authors: Alessandro
authors: A
authors: Florio
authors: Department of Biology, University of Florence, Florence, Italy.
authors: Marco
authors: M
authors: Bazzicalupo
authors: Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per lo studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Rome, Italy.
authors: Anna
authors: A
authors: Benedetti
authors: Consiglio per la Ricerca e la sperimentazione in Agricoltura, Centro di Ricerca per l'Agrobiologia e la Pedologia (CRA-ABP), Florence, Italy.
authors: Stefano
authors: S
authors: Mocali
mesh_terms: D000150:Acinetobacter / Q000378:metabolism; D019295:Computational Biology; D030541:Databases, Genetic; D004925:Escherichia / Q000378:metabolism; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D053858:Metabolic Networks and Pathways; D046228:Microarray Analysis / Q000379:methods*; D008958:Models, Molecular; D010641:Phenotype; D020579:Sinorhizobium / Q000378:metabolism; D012984:Software; D017355:Zymomonas / Q000378:metabolism
keywords: Genomics; KEGG; Metabolism; Phenomics; Phenotype Microarray