Mercurial > repos > peterjc > secreted_protein_workflow
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| author | peterjc |
|---|---|
| date | Fri, 25 Oct 2013 10:24:35 -0400 |
| parents | 72f03c2102ee |
| children |
| rev | line source |
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| 1 | 1 This is package is a Galaxy workflow for the identification of candidate |
| 2 secreted proteins from a given protein FASTA file. | |
| 3 | |
| 4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a | |
| 5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001) | |
| 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. (2011), and is a simplification of |
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3a0c0d1c388f
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8 the candidate effector protocol described in Jones et al. (2009). |
| 1 | 9 |
| 10 See http://www.galaxyproject.org for information about the Galaxy Project. | |
| 11 | |
| 12 | |
| 4 | 13 Availability |
| 14 ============ | |
| 15 | |
| 16 This workflow is available to download and/or install from the main | |
| 17 Galaxy Tool Shed: | |
| 18 | |
| 19 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow | |
| 20 | |
| 21 Test releases (which should not normally be used) are on the Test Tool Shed: | |
| 22 | |
| 23 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow | |
| 24 | |
| 25 Development is being done on github here: | |
| 26 | |
| 27 https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow | |
| 28 | |
| 29 | |
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30 Sample Data |
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31 =========== |
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32 |
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33 This workflow was developed and run on several nematode species. For example, |
| 4 | 34 try the protein set for *Bursaphelenchus xylophilus* (Kikuchi et al. 2011): |
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35 |
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36 ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz |
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peterjc
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37 |
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38 You can upload this directly into Galaxy via this URL. Galaxy will handle |
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39 removing the gzip compression to give you the FASTA protein file which has |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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40 18,074 sequences. The expected result (selecting organism type Eukaryote) |
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3a0c0d1c388f
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41 is a FASTA protein file of 2,297 predicted secreted protein sequences. |
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42 |
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43 |
| 1 | 44 Citation |
| 45 ======== | |
| 46 | |
| 47 If you use this workflow directly, or a derivative of it, in work leading | |
| 48 to a scientific publication, please cite: | |
| 49 | |
| 4 | 50 Cock, P.J.A. and Pritchard, L. (2014). Galaxy as a platform for identifying |
| 1 | 51 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions: |
| 4 | 52 Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds. |
| 53 Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7. | |
| 54 http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7 | |
| 1 | 55 |
| 4 | 56 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
| 57 Galaxy tools and workflows for sequence analysis with applications | |
| 58 in molecular plant pathology. PeerJ 1:e167 | |
| 59 http://dx.doi.org/10.7717/peerj.167 | |
| 1 | 60 |
| 61 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004) | |
| 62 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95. | |
| 63 http://dx.doi.org/10.1016/j.jmb.2004.05.028 | |
| 64 | |
| 65 Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001) | |
| 66 Predicting transmembrane protein topology with a hidden Markov model: | |
| 67 application to complete genomes. J Mol Biol 305: 567- 580. | |
| 68 http://dx.doi.org/10.1006/jmbi.2000.4315 | |
| 69 | |
| 70 | |
| 71 Additional References | |
| 72 ===================== | |
| 73 | |
| 74 Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011) | |
| 75 Genomic insights into the origin of parasitism in the emerging plant | |
| 4 | 76 pathogen *Bursaphelenchus xylophilus*. PLoS Pathog 7: e1002219. |
| 1 | 77 http://dx.doi.org/10.1371/journal.ppat.1002219 |
| 78 | |
| 79 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009) | |
| 80 Identification and functional characterization of effectors in expressed | |
| 81 sequence tags from various life cycle stages of the potato cyst nematode | |
| 4 | 82 *Globodera pallida*. Mol Plant Pathol 10: 815–28. |
| 1 | 83 http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x |
| 84 | |
| 85 | |
| 86 Dependencies | |
| 87 ============ | |
| 88 | |
| 89 These dependencies should be resolved automatically via the Galaxy Tool Shed: | |
| 90 | |
| 91 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp | |
| 92 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id | |
| 93 | |
| 94 However, at the time of writing those Galaxy tools have their own | |
| 95 dependencies required for this workflow which require manual | |
| 96 installation (SignalP v3.0 and TMHMM v2.0). | |
| 97 | |
| 98 | |
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99 History |
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peterjc
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100 ======= |
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101 |
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102 ======= ====================================================================== |
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103 Version Changes |
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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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104 ------- ---------------------------------------------------------------------- |
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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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105 v0.0.1 - Initial release to Tool Shed (May, 2013) |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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106 - Expanded README file to include example data |
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3a0c0d1c388f
Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
peterjc
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107 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter |
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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
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108 tool to avoid warning about new ``header_lines`` parameter. |
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109 - Added link to Tool Shed in the workflow annotation explaining there |
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72f03c2102ee
Uploaded v0.0.2b, adding link to Tool Shed in the workflow annotation (so that end users can find the README file).
peterjc
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110 is a README file with sample data, and a requested citation. |
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3a0c0d1c388f
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111 ======= ====================================================================== |
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112 |
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113 |
| 1 | 114 Developers |
| 115 ========== | |
| 116 | |
| 117 This workflow is under source code control here: | |
| 118 | |
| 4 | 119 https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow |
| 1 | 120 |
| 121 To prepare the tar-ball for uploading to the Tool Shed, I use this: | |
| 122 | |
| 123 $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga | |
| 124 | |
| 125 Check this, | |
| 126 | |
| 127 $ tar -tzf secreted_protein_workflow.tar.gz | |
| 128 README.rst | |
| 129 repository_dependencies.xml | |
| 130 secreted_protein_workflow.ga |