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GeneViTo: visualizing gene-product functional and structural features in genomic datasets

TitleGeneViTo: visualizing gene-product functional and structural features in genomic datasets
Publication TypeJournal Article
Year of Publication2003
AuthorsVernikos, G. S., C. G. Gkogkas, V. J. Promponas, and S. J. Hamodrakas
JournalBMC bioinformatics
Date PublishedOct 31
ISBN Number1471-2105; 1471-2105
KeywordsBacterial, Bacterial Proton-Translocating ATPases/chemistry/physiology, Bacterial/genetics, Bacterial/genetics/physiology, Base Sequence/genetics, Binding Sites/genetics, Chlamydia trachomatis/enzymology/genetics, Chromosome Mapping/methods, Chromosomes, Computational Biology/methods, Computer Graphics/trends, Databases, DNA Restriction Enzymes/genetics, Genes, Genetic, Genome, Methanococcus/enzymology/genetics, Molecular Sequence Data, Phylogeny, Protein Subunits/genetics, RNA, rRNA/genetics, Software, Transfer/genetics, User-Computer Interface

BACKGROUND: The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. RESULTS: GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. CONCLUSIONS: GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment is already installed in the system.

by Dr. Radut.