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- Title
CiVi: circular genome visualization with unique features to analyze sequence elements.
- Authors
Overmars, Lex; van Hijum, Sacha A. F. T.; Siezen, Roland J.; Francke, Christof
- Abstract
Summary: 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.
- Subjects
NUCLEOTIDE sequence; MICROBIAL genomes; GENE expression; GENE mapping; DATA integration
- Publication
Bioinformatics, 2015, Vol 31, Issue 17, p2867
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btv249