title: inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons.
abstract: BACKGROUND
  Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines.
  
  
  RESULTS
  InGeno provides a user-friendly interactive visualization platform for sequence comparisons (comprehensive reciprocal protein--protein comparisons) between complete genome sequences and all associated annotations and features. The comparison data can be acquired from several different sequence analysis programs in flexible formats. Automatic dot-plot analysis includes output reduction, filtering, ortholog testing and linear regression, followed by smart clustering (local collinear blocks; LCBs) to reveal similar genome regions. Further, the system provides genome alignment and visualization editor, collinear relationships and strain-specific islands. Specific annotations and functions are parsed, recognized, clustered, logically concatenated and visualized and summarized in reports.
  
  
  CONCLUSIONS
  As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) and has been proven to be sensitive and accurate. This modular software is user-friendly and easily accommodates new routines to meet specific user-defined requirements.
authors.affiliation: Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany. liang@biozentrum.uni-wuerzburg.de
authors.forename: Chunguang
authors.initials: C
authors.lastname: Liang
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
mesh_terms: D001483:Base Sequence; D004925:Escherichia / Q000235:genetics / Q000378:metabolism / Q000472:pathogenicity; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D008087:Listeria / Q000235:genetics; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D013045:Species Specificity