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SynMap2 and SynMap3D: web-based whole-genome synteny browsers
Abstract
Summary: Current synteny visualization tools either focus on small regions of sequence and do not illustrate genome-wide trends, or are complicated to use and create visualizations that are difficult to interpret. To address this challenge, The Comparative Genomics Platform (CoGe) has developed two web-based tools to visualize synteny across whole genomes. SynMap2 and SynMap3D allow researchers to explore whole genome synteny patterns (across two or three genomes, respectively) in responsive, web-based visualization and virtual reality environments. Both tools have access to the extensive CoGe genome database (containing over 30 000 genomes) as well as the option for users to upload their own data. By leveraging modern web technologies there is no installation required, making the tools widely accessible and easy to use. Availability and Implementation: Both tools are open source (MIT license) and freely available for use online through CoGe (https://genomevolution.org). SynMap2 and SynMap3D can be accessed at http://genomevolution.org/coge/SynMap.pl and http://genomevolution.org/coge/SynMap3D.pl, respectively. Source code is available: https://github.com/LyonsLab/coge. Supplementary information: Supplementary data are available at Bioinformatics online.
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“The physical position of homologs offers a second line of evidence that can help overcome challenges posed by WGDs, tandem arrays, heterozygous-duplicated regions, and other genomic complexities (Drillon et al., 2020; Haug-Baltzell et al., 2017; Wang et al., 2012).”
From GENESPACE tracks regions of interest and gene copy number variation across multiple genomes (2022) · cites this paper as Haug-Baltzell et al., 2017
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Research works printed but not linked: 7
- Cabanier, 2015, HTML Canvas 2D Context
- Dahlström, 2011, Scalable Vector Graphics (SVG) 1.1
- Edelsbrunner, 2010, Computational topology: an introduction, Am. Math. Soc
- Krzywinski, 2009, Circos: An information aesthetic for comparative genomics, Genome Res, 19, 1639, 10.1101/gr.092759.109 · DOI
- Lyons, 2008, How to usefully compare homologous plant genes and chromosomes as DNA sequences, Plant J, 53, 661, 10.1111/j.1365-313X.2007.03326.x · DOI
- Lyons, 2008, The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids, Trop. Plant Biol, 1, 181, 10.1007/s12042-008-9017-y · DOI
- McKay, 2010, Using the Generic Synteny Browser (GBrowse_syn), Curr. Protoc. Bioinformatics, 10.1002/0471250953.bi0912s31 · DOI
Cited by
Sorted by citations
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
Lovell, J. T., Sreedasyam, A., Schranz, M. E., Wilson, M., Carlson, J. W., Harkess, A., Emms, D., Goodstein, D. M., & Schmutz, J. (2022) · eLife · doi:10.7554/elife.78526 · Cited by 391
Chan, V. S., Mohamed, F. B., Salleh, F. B. M., Iglesias, A., Abdul-Rahman, A., Miga, M., Najjar, F. H., & Cao, C. (2026) · Information Visualization · doi:10.1177/14738716261498353
Metadata
- Authors
- Haug-Baltzell, A., Stephens, S. A., Davey, S., Scheidegger, C. E., & Lyons, E.
- Affiliations
- Genetics GIDP, University of Arizona, Tucson AZ, USA
- Department of Computer Science, University of Arizona, Tucson AZ, USA
- BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson AZ, USA
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-03-16
- Volume
- 33
- Issue
- 14
- Pages
- 2197-2198
- ISSN
- 1367-4803
- 1367-4811
- Cited by
- 181
- References
- 0
- Language
- en
- Funders
- National Science Foundation (IOS—1339156, IOS—1444490)
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