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. 2009 Sep;7(3):143-6.
doi: 10.1016/S1672-0229(08)60043-1.

3D genome tuner: compare multiple circular genomes in a 3D context

Qi Wang  1 , Qun Liang, Xiuqing Zhang
Affiliations

3D genome tuner: compare multiple circular genomes in a 3D context

Qi Wang et al. Genomics Proteomics Bioinformatics. 2009 Sep.

Abstract

Circular genomes, being the largest proportion of sequenced genomes, play an important role in genome analysis. However, traditional 2D circular map only provides an overview and annotations of genome but does not offer feature-based comparison. For remedying these shortcomings, we developed 3D Genome Tuner, a hybrid of circular map and comparative map tools. Its capability of viewing comparisons between multiple circular maps in a 3D space offers great benefits to the study of comparative genomics. The program is freely available (under an LGPL licence) at http://sourceforge.net/projects/dgenometuner.

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Figures

Fig. 1
Figure 1
From linear view (A) to 2D circular view (B) then 3D circular view (C). The lines linking homologous regions are condensed to offer a clearer comparison.
Fig. 2
Figure 2
A screenshot showing comparison between two mitochondrion genomes from Homo sapiens (AC_000021) and Mus musculus domesticus (NC_006914). The tracks from the outside to inside represent: coordinates; CDSs; homologous regions calculated by NUCmer; GC-content; tRNA and rRNA genes; GC-skew [(G−C)/(G+C)]. Lines linking the upper and lower circular maps are BLAST alignments between the orthologous genes.
See this image and copyright information in PMC

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