Intern
    Sonderforschungsbereich Transregio 34

    GENOVA

    A rapid genome visualization and analysis software for detailed comparison of genome functions - GENOVA

    Chunguang Liang, Silvia Herbert, Christine Wölz, Jörg Bernhardt, Susanne Engelmann, Michael Hecker, Friedrich Götz and Thomas Dandekar

    Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany

    liang@biozentrum.uni-wuerzburg.de; dandekar@biozentrum.uni-wuerzburg.de

    Introduction

    Genova is a JAVA-base software to manage, edit, visualize and store the genome sequence locally. All genes or ORFs are categorized by their function and plotted with different colours in a map. Support toolkit includes a sequence-format conversion tool and a sequence GC percent analysis/visualization tool. The software is designed for genome sequence comparisons, which has been proven to be powerful, in particular to prokaryotic genomes of close phylogenetic distances.

    GENOVA is implemented in JAVA 6 for a platform-independency. BioJava 1.6 is used for rapid querying, extracting and restoring the sequence features. Sequence files of rich-format can be readily parsed with the BioJavax extension. GENOVA software allows users to filter, query and edit the annotation record in a table. Moreover, people can assign a desired functional category for each entry, which will be marked in a certain colour from the palette. Simultaneously the software draws its genome map according to the user modification. GENOVA provides a couple of sequence analysis tools within the workbench, JFreeChart library is applied for the interactive visualization of the results. Noia IDE icons have been integrated into the package. The GENOVA software is released under a GNU Lesse General Public License (LGPL).

    Downloads

    Win XP, 2003: Genova.rar Linux system: Genova.tar.gz General Unix: Genova.zipSource code : genovasrc.zip, the latest source code has been enclosed into the Genova.rar package.Tutorial doc: Genova-tutorial.pdfSample files: sauRN1_COLOR.gbk, Vaccinia GLV-1h68

    All the download links will be publicly available once the paper is accepted. The other sample files, e.g., GLV-1h68, will be subsequently available if the genome is published. GENOVA requires the Java Runtime Environment 1.6, which can be found at http://java.sun.com/javase/downloads/index.jsp

    Analysis screenshots

    Fig. Genome funcion canvas applying GENOVA on Vaccinia virus GLV-1h68 [Large]

    Fig. Genome GC% content visualization on Vaccinia GLV-1h68

    Fig. Pathogenicity island analysis of Staphylococcus aureus RN1 [Large,Large]

    Fig. RsbU loci restoration in Staphyloccocus aureus RN1HG genome [Large].

    Fig. Genome feature editor of GENOVA [Large].

    Funding

    This project is supported by Deutsche Forschungsgemeinschaft (German Research Foundation: TR 34-A5, SFB 630-C6, SFB688-A2, SPP1316), BMBF (FUNCRYPTA) and Land Bavaria.