CiVi: circular genome visualization with unique features to analyze sequence elements

被引：30

作者：

Overmars, Lex ^{[1
,2
,3
]}

van Hijum, Sacha A. F. T. ^{[1
,2
,4
]}

Siezen, Roland J. ^{[1
,2
]}

Francke, Christof ^{[1
,2
,5
]}

机构：

[1] Radboud Univ Nijmegen, Med Ctr, CMBI, NL-6525 GA Nijmegen, Netherlands

[2] Netherlands Bioinformat Ctr, NL-6500 HB Nijmegen, Netherlands

[3] Univ Amsterdam, Inst Biodivers & Ecosyst Dynam, Amsterdam, Netherlands

[4] NIZO Food Res BV, Ede, Netherlands

[5] Hgsch Arnhem Nijmegen, Bioctr, NL-6525 EM Nijmegen, Netherlands

来源：

BIOINFORMATICS | 2015年 / 31卷 / 17期

关键词：

CGVIEW; VIEWER; TOOL;

D O I：

10.1093/bioinformatics/btv249

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2867 / 2869

页数：3

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