FractBias: A graphical tool for assessing fractionation bias following polyploidy

Blake L. Joyce, Asher Haug-Baltzell, Sean Davey, Matthew Bomhoff, James C. Schnable, Eric H Lyons

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns. We have developed a tool, FractBias, to calculate and visualize gene retention and fractionation patterns across whole genomes. Through integration with SynMap and its parent platform CoGe, assembled genomes are pre-loaded and available for analysis, as well as letting researchers integrate their own data with security options to keep them private or make them publicly available.

Original languageEnglish (US)
Pages (from-to)552-554
Number of pages3
JournalBioinformatics
Volume33
Issue number4
DOIs
StatePublished - Feb 15 2017

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Polyploidy
Fractionation
Genome
Genes
Gene
Computer Security
Post-processing
Chromosome
Chromosomes
Integrate
Research Personnel
Graphics
Calculate

ASJC Scopus subject areas

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

Cite this

FractBias : A graphical tool for assessing fractionation bias following polyploidy. / Joyce, Blake L.; Haug-Baltzell, Asher; Davey, Sean; Bomhoff, Matthew; Schnable, James C.; Lyons, Eric H.

In: Bioinformatics, Vol. 33, No. 4, 15.02.2017, p. 552-554.

Research output: Contribution to journalArticle

Joyce, BL, Haug-Baltzell, A, Davey, S, Bomhoff, M, Schnable, JC & Lyons, EH 2017, 'FractBias: A graphical tool for assessing fractionation bias following polyploidy', Bioinformatics, vol. 33, no. 4, pp. 552-554. https://doi.org/10.1093/bioinformatics/btw666
Joyce, Blake L. ; Haug-Baltzell, Asher ; Davey, Sean ; Bomhoff, Matthew ; Schnable, James C. ; Lyons, Eric H. / FractBias : A graphical tool for assessing fractionation bias following polyploidy. In: Bioinformatics. 2017 ; Vol. 33, No. 4. pp. 552-554.
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