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Galaxy as a Platform for Identifying Candidate Pathogen Effectors

  • Peter J. A. CockEmail author
  • Leighton Pritchard
Part of the Methods in Molecular Biology book series (MIMB, volume 1127)

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 workflows, and shared with other Galaxy users, allowing them to easily perform the same analysis or protocol on their own data.

We describe example Galaxy workflows for the identification 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.

Key words

Effectors Workflow Pipeline Galaxy Classification Bioinformatics Sequence analysis Genomics High-throughput screening 

Notes

Acknowledgments

The James Hutton Institute receives funding from the Scottish Government.

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Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  1. 1.Information and Computational SciencesThe James Hutton InstituteDundeeUK

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