view README.txt @ 2:aecb871dfe4c draft

Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
author peterjc
date Mon, 08 Jul 2013 11:19:47 -0400
parents 9f2fea8a5d32
children 237d3bef3b86
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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


Dependencies
============

These dependencies should be resolved automatically via the Galaxy Tool Shed:
 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id

However, at the time of writing those Galaxy tools have their own dependencies
required for this workflow which require manual installation (SignalP v3.0
and TMHMM v2.0).


Development
===========

To prepare the tar-ball for uploading to the Tool Shed, I use this:

$ tar -cf secreted_protein_workflow.tar.gz README.txt repository_dependencies.xml secreted_protein_workflow.ga

Check this,

$ tar -tzf secreted_protein_workflow.tar.gz 
README.txt
repository_dependencies.xml
secreted_protein_workflow.ga