title: Galaxy as a platform for identifying candidate pathogen effectors.
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.
authors.affiliation: Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK, peter.cock@hutton.ac.uk.
authors.forename: Peter J A
authors.initials: PJ
authors.lastname: Cock
authors.forename: Leighton
authors.initials: L
authors.lastname: Pritchard
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D015801:Helminth Proteins / Q000737:chemistry / Q000378:metabolism*; D020407:Internet; D008969:Molecular Sequence Data; D009348:Nematoda / Q000378:metabolism* / Q000472:pathogenicity*; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D015801:Helminth Proteins