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. 2011 Apr 1;27(7):1009-10.
doi: 10.1093/bioinformatics/btr039. Epub 2011 Jan 28.

Easyfig: A Genome Comparison Visualizer

Free PMC article

Easyfig: A Genome Comparison Visualizer

Mitchell J Sullivan et al. Bioinformatics. .
Free PMC article


Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface. BLAST comparisons between multiple genomic regions, ranging from single genes to whole prokaryote chromosomes, can be generated, visualized and interactively coloured, enabling a rapid transition between analysis and the preparation of publication quality figures.

Availability: Easyfig is freely available (under a GPL license) for download (for Mac OS X, Unix and Microsoft Windows) from the SourceForge web site:


Fig. 1.
Fig. 1.
Comparison between the genomes of Escherichia coli O157:H7 str. EDL933 (top), E.coli O157:H7 str. Sakai (middle) and E.coli K12 str. MG1655 (bottom). (A) Whole-genome comparison with prophage regions shown as purple boxes. (B) A zoomed-in view showing that prophages have inserted at tRNA-Ser in the O157:H7 strains EDL933 and Sakai (prophages CP933M and Sp4, respectively), but not in K12. Dashed red lines indicate the site in the whole-genome sequences of the prophages and flanking genes shown in the bottom figure. Vertical blocks between sequences indicate regions of shared similarity shaded according to BLASTn (blue for matches in the same direction or orange for inverted matches). CDS in prophage Sp4 have been coloured according to Asadulghani et al. (2009) and functions of the CDS in CP933M have been inferred from BLAST hits and existing annotation.

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    1. Altschul S.F., et al. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. - PubMed
    1. Asadulghani M., et al. The defective prophage pool of Escherichia coli O157: prophage-prophage interactions and horizontal transfer of virulence determinants. PLoS Pathog. 2009;5:e1000408. - PMC - PubMed
    1. Carver T., et al. ACT: the artemis comparison tool. Bioinformatics. 2005;21:3422–3423. - PubMed
    1. Darling A.E., et al. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010;5:e11147. - PMC - PubMed
    1. Guy L., et al. genoPlotR: comparative gene and genome visualization in R. Bioinformatics. 2010;26:2334–2335. - PMC - PubMed

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