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

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

Research output: Contribution to journalArticle

20 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)2197-2198
Number of pages2
JournalBioinformatics
Volume33
Issue number14
DOIs
StatePublished - Jul 15 2017

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Synteny
Web-based
Genome
Genes
Comparative Genomics
Visualization
Genomics
Virtual Reality
Virtual reality
Research Personnel
Databases
Technology

ASJC Scopus subject areas

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

SynMap2 and SynMap3D : Web-based whole-genome synteny browsers. / Haug-Baltzell, Asher; Stephens, Sean A.; Davey, Sean; Scheidegger, Carlos Eduardo; Lyons, Eric H.

In: Bioinformatics, Vol. 33, No. 14, 15.07.2017, p. 2197-2198.

Research output: Contribution to journalArticle

Haug-Baltzell, Asher ; Stephens, Sean A. ; Davey, Sean ; Scheidegger, Carlos Eduardo ; Lyons, Eric H. / SynMap2 and SynMap3D : Web-based whole-genome synteny browsers. In: Bioinformatics. 2017 ; Vol. 33, No. 14. pp. 2197-2198.
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