SynMap2 and SynMap3D: Web-based whole-genome synteny browsers

Asher Haug-Baltzell; Sean A. Stephens; Sean Davey; Carlos E. Scheidegger; Eric Lyons

doi:10.1093/bioinformatics/btx144

SynMap2 and SynMap3D: Web-based whole-genome synteny browsers

Asher Haug-Baltzell
, Sean A. Stephens
, Sean Davey
, Carlos E. Scheidegger
, Eric Lyons

Research output: Contribution to journal › Article › peer-review

122 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	2197-2198
Number of pages	2
Journal	Bioinformatics
Volume	33
Issue number	14
DOIs	https://doi.org/10.1093/bioinformatics/btx144
State	Published - Jul 15 2017

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btx144

Cite this

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abstract = "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.",

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AU - Scheidegger, Carlos E.

AU - Lyons, Eric

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SynMap2 and SynMap3D: Web-based whole-genome synteny browsers

Abstract

ASJC Scopus subject areas

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