SynMap2 and SynMap3D: web-based whole-genome synteny browsers.
CONCLUSIONS
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.


METHODS
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 .


BACKGROUND
ericlyons@email.arizona.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Genetics GIDP, University of Arizona, Tucson AZ, USA.
Asher
A
Haug-Baltzell
Department of Computer Science, University of Arizona, Tucson AZ, USA.
Sean A
SA
Stephens
BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson AZ, USA.
Sean
S
Davey
Department of Computer Science, University of Arizona, Tucson AZ, USA.
Carlos E
CE
Scheidegger
Genetics GIDP, University of Arizona, Tucson AZ, USA.|BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson AZ, USA.
Eric
E
Lyons
D016678:Genome; D023281:Genomics / Q000379:methods*; D012984:Software; D026801:Synteny; D064878:Web Browser; D000073336:Whole Genome Sequencing