view README.md @ 0:3a6de5cb858d draft

Uploaded first attempt at a workflow with dependencies on the Tool Shed

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. This workflow was used in Kikuchi et al (2001), and is a simplification of the candidate effector protocol described in Jones et al (2009).

Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, et al. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219.
http://dx.doi.org/10.1371/journal.ppat.1002219

Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, Castelli L, et al. (2009) Identification and functional characterization of effectors in expressed sequence tags from various life cycle stages of the potato cyst nematode Globodera pallida. Mol Plant Pathol 10: 815–28.
http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x

Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
http://dx.doi.org/10.1016/j.jmb.2004.05.028

Krogh A, Larsson B, von Heijne G, Sonnhammer E (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567- 580.
http://dx.doi.org/10.1006/jmbi.2000.4315


Availability
============

This workflow is available on the main Galaxy Tool Shed:
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow

Development is being done on github here:
https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow