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1 This is package is a Galaxy workflow for the identification of candidate
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2 secreted proteins from a given protein FASTA file.
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3
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4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
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5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
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6 on those, and selects only proteins without a predicted trans-membrane helix.
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7 This workflow was used in Kikuchi et al (2001), and is a simplification of
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8 the candidate effector protocol described in Jones et al (2009).
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9
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10 See http://www.galaxyproject.org for information about the Galaxy Project.
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11
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12
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13 Citation
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14 ========
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15
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16 If you use this workflow directly, or a derivative of it, in work leading
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17 to a scientific publication, please cite:
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18
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19 Cock, P.J.A. and Pritchard, L. 2013. Galaxy as a platform for identifying
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20 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
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21 Methods and Protocols (Second Edition)"; Methods in Molecular Biology.
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22 Humana Press, Springer. In press.
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23
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24 Also consider citing:
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25
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26 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
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27 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
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28 http://dx.doi.org/10.1016/j.jmb.2004.05.028
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29
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30 Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001)
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31 Predicting transmembrane protein topology with a hidden Markov model:
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32 application to complete genomes. J Mol Biol 305: 567- 580.
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33 http://dx.doi.org/10.1006/jmbi.2000.4315
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34
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35
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36 Additional References
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37 =====================
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38
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39 Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011)
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40 Genomic insights into the origin of parasitism in the emerging plant
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41 pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219.
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42 http://dx.doi.org/10.1371/journal.ppat.1002219
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43
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44 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)
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45 Identification and functional characterization of effectors in expressed
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46 sequence tags from various life cycle stages of the potato cyst nematode
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47 Globodera pallida. Mol Plant Pathol 10: 815–28.
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48 http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x
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49
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50
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51 Availability
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52 ============
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53
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54 This workflow is available to download and/or install from the main
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55 Galaxy Tool Shed:
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56
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57 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
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58
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59 Test releases (which should not normally be used) are on the Test Tool Shed:
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60
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61 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
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62
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63 Development is being done on github here:
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64
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65 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
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66
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67
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68 Dependencies
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69 ============
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70
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71 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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72
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73 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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74 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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75
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76 However, at the time of writing those Galaxy tools have their own
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77 dependencies required for this workflow which require manual
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78 installation (SignalP v3.0 and TMHMM v2.0).
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79
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80
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81 Developers
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82 ==========
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83
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84 This workflow is under source code control here:
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85
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86 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow
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87
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88 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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89
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90 $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga
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91
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92 Check this,
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93
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94 $ tar -tzf secreted_protein_workflow.tar.gz
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95 README.rst
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96 repository_dependencies.xml
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97 secreted_protein_workflow.ga
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