Galaxy as a platform for identifying candidate pathogen effectors

Peter J.A. Cock, Leighton Pritchard

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Citations (Scopus)

Abstract

The Galaxy web platform provides an integrated system for its users to run multiple computational tools, linking their output in order to perform sophisticated analysis without requiring any programming or installation of software beyond a modern web-browser. Analyses can be saved as reusable workfl ows, and shared with other Galaxy users, allowing them to easily perform the same analysis or protocol on their own data. We describe example Galaxy workfl ows for the identifi cation of candidate pathogen effector proteins. Our main example focuses on nematode plant pathogens where signal peptide and transmembrane prediction tools are used to identify predicted secreted proteins.

Original languageEnglish
Title of host publicationPlant-Pathogen Interactions
Subtitle of host publicationMethods and Protocols
EditorsPaul Birch, John T. Jones, Jorunn I.B. Bos
Place of PublicationNew York
PublisherSpringer
Chapter1
Pages3-15
Number of pages13
Edition2nd
ISBN (Print)9781627039864, 9781627039857
DOIs
Publication statusPublished - 19 Mar 2014

Publication series

NameMethods in Molecular Biology
PublisherSpringer Verlag
Volume1127
ISSN (Print)1064-3745

    Fingerprint

Keywords

  • bioinformatics
  • classification
  • effectors
  • Galaxy
  • genomics
  • high-throughput screening
  • pipeline
  • sequence analysis
  • workflow

Cite this

Cock, P. J. A., & Pritchard, L. (2014). Galaxy as a platform for identifying candidate pathogen effectors. In P. Birch, J. T. Jones, & J. I. B. Bos (Eds.), Plant-Pathogen Interactions: Methods and Protocols (2nd ed., pp. 3-15). (Methods in Molecular Biology; Vol. 1127). New York: Springer. https://doi.org/10.1007/978-1-62703-986-4_1