title: CiVi: circular genome visualization with unique features to analyze sequence elements.
abstract: We have developed CiVi, a user-friendly web-based tool to create custom circular maps to aid the analysis of microbial genomes and sequence elements. Sequence related data such as gene-name, COG class, PFAM domain, GC%, and subcellular location can be comprehensively viewed. Quantitative gene-related data (e.g. expression ratios or read counts) as well as predicted sequence elements (e.g. regulatory sequences) can be uploaded and visualized. CiVi accommodates the analysis of genomic elements by allowing a visual interpretation in the context of: (i) their genome-wide distribution, (ii) provided experimental data and (iii) the local orientation and location with respect to neighboring genes. CiVi thus enables both experts and non-experts to conveniently integrate public genome data with the results of genome analyses in circular genome maps suitable for publication.
  
  
  BACKGROUND
  L.Overmars@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
  
  
  METHODS
  CiVi is freely available at http://civi.cmbi.ru.nl.
authors.affiliation: CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands, Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands.
authors.forename: Lex
authors.initials: L
authors.lastname: Overmars
authors.affiliation: CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands, Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands, NIZO Food Research B.V., Ede, The Netherlands and.
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
authors.affiliation: CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands, Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands.
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
authors.affiliation: CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands, Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands, Hogeschool Arnhem en Nijmegen BioCentre, 6525EM Nijmegen, The Netherlands.
authors.forename: Christof
authors.initials: C
authors.lastname: Francke
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D030541:Databases, Genetic; D005798:Genes, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D016247:Information Storage and Retrieval; D058977:Molecular Sequence Annotation / Q000379:methods*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012984:Software; D014584:User-Computer Interface