Lex Overmars1, Sacha A F T van Hijum2, Roland J Siezen3, Christof Francke4. 1. 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. 2. 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. 3. CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands, Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands. 4. 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.
Abstract
UNLABELLED: 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. CONTACT: L.Overmars@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. AVAILABILITY AND IMPLEMENTATION: CiVi is freely available at http://civi.cmbi.ru.nl.
UNLABELLED: 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. CONTACT: L.Overmars@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. AVAILABILITY AND IMPLEMENTATION:CiVi is freely available at http://civi.cmbi.ru.nl.
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