| This Tool Shed Repository contains a workflow for the identification of candidate secreted proteins from a given protein FASATA file. It runs SignalP v3.0 and selects only proteins with a strong predicted signal peptide, and then runs TMHMM v2.0 on those, and selects only proteins without a predicted trans-membrane helix. See the README file for more details.
Citation: Cock, P.J.A. and Pritchard, L. (2014). Galaxy as a platform for identifying candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds. Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7. http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7 |
hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/secreted_protein_workflow