| This runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001) on those, and selects only proteins without a predicted trans-membrane helix. This workflow was used in Kikuchi et al. (2011), and is a simplification of the candidate effector protocol described in Jones et al. (2009). |
hg clone https://testtoolshed.g2.bx.psu.edu/repos/peterjc/secreted_protein_workflow