Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jun 4:6:e4958.
doi: 10.7717/peerj.4958. eCollection 2018.

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

Floréal Cabanettes  1 , Christophe Klopp  1
Affiliations

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

Floréal Cabanettes et al. PeerJ. .

Abstract

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

Keywords: Dot plot; Genome assessment; Interactive user interface; Large genomes.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1. Results page view.
(A) Main menu to navigate D-GENIES pages. (B) Reference and query sequence drop down selection boxes and button to zoom in the alignment. (C) Export menu to download image files (PNG and SVG), alignment, ordered query and unaligned query or reference FASTA files. (D) Identity color panel. (E) Match size filtering slider. (F) Identity filtering entry and check boxes. (G) Strong precision check-box. (H) Line width slider. (I) Reference and query border horizontal and vertical border line slider. (J) Query sort and unsort button. (K) Noise filtering button. (L) Similarity summary button. (M) Delete job button.
Figure 2
Figure 2. Example of identity summary.
See this image and copyright information in PMC

References

    1. Brodie R, Roper RL, Upton C. Jdotter: a Java interface to multiple dotplots generated by dotter. Bioinformatics. 2004;20(2):279–281. doi: 10.1093/bioinformatics/btg406. - DOI - PubMed
    1. Bostock M, Ogievetsky V, Heer J. D3 Data-Driven Documents. IEEE Transactions on Visualization and Computer Graphics. 2011;17(12):2301–2309. doi: 10.1109/TVCG.2011.185. - DOI - PubMed
    1. Husemann P, Stoye J. r2cat: synteny plots and comparative assembly. Bioinformatics. 2009;26(4):570–571. doi: 10.1093/bioinformatics/btp690. - DOI - PMC - PubMed
    1. Krumsiek J, Arnold R, Rattei T. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics. 2007;23(8):1026–1028. doi: 10.1093/bioinformatics/btm039. - DOI - PubMed
    1. Kumar S, Stecher G, Suleski M, Hedges SB. TimeTree: a resource for timelines, timetrees, and divergence times. Molecular Biology and Evolution. 2017;34(7):1812–1819. doi: 10.1093/molbev/msx116. - DOI - PubMed

LinkOut - more resources