title: Insyght: navigating amongst abundant homologues, syntenies and gene functional annotations in bacteria, it's that symbol!
abstract: High-throughput techniques have considerably increased the potential of comparative genomics whilst simultaneously posing many new challenges. One of those challenges involves efficiently mining the large amount of data produced and exploring the landscape of both conserved and idiosyncratic genomic regions across multiple genomes. Domains of application of these analyses are diverse: identification of evolutionary events, inference of gene functions, detection of niche-specific genes or phylogenetic profiling. Insyght is a comparative genomic visualization tool that combines three complementary displays: (i) a table for thoroughly browsing amongst homologues, (ii) a comparator of orthologue functional annotations and (iii) a genomic organization view designed to improve the legibility of rearrangements and distinctive loci. The latter display combines symbolic and proportional graphical paradigms. Synchronized navigation across multiple species and interoperability between the views are core features of Insyght. A gene filter mechanism is provided that helps the user to build a biologically relevant gene set according to multiple criteria such as presence/absence of homologues and/or various annotations. We illustrate the use of Insyght with scenarios. Currently, only Bacteria and Archaea are supported. A public instance is available at http://genome.jouy.inra.fr/Insyght. The tool is freely downloadable for private data set analysis.
authors.affiliation: INRA, UR 1077 Mathématique Informatique et Génome, 78352 Jouy-en-Josas, France thomas.lacroix@jouy.inra.fr.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lacroix
authors.affiliation: INRA, UR 1077 Mathématique Informatique et Génome, 78352 Jouy-en-Josas, France.
authors.forename: Valentin
authors.initials: V
authors.lastname: Loux
authors.affiliation: INRA, UR 1077 Mathématique Informatique et Génome, 78352 Jouy-en-Josas, France.
authors.forename: Annie
authors.initials: A
authors.lastname: Gendrault
authors.affiliation: CNRS, UPMC, FR2424, ABiMS, Station Biologique, 29680 Roscoff, France.
authors.forename: Mark
authors.initials: M
authors.lastname: Hoebeke
authors.affiliation: INRA, UR 1077 Mathématique Informatique et Génome, 78352 Jouy-en-Josas, France.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Gibrat
mesh_terms: D003196:Computer Graphics; D057225:Data Mining / Q000379:methods*; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D023281:Genomics / Q000379:methods*; D058977:Molecular Sequence Annotation; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D026801:Synteny