Mercurial > repos > peterjc > secreted_protein_workflow
annotate README.txt @ 3:237d3bef3b86 draft
Uploaded v0.0.1c, README formatting changes
| author | peterjc |
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| date | Mon, 08 Jul 2013 12:59:49 -0400 |
| parents | aecb871dfe4c |
| children |
| rev | line source |
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| 3 | 1 This is package is a Galaxy workflow for the identification of candidate |
| 2 secreted proteins from a given protein FASATA file. | |
| 3 | |
| 4 It runs SignalP v3.0 and selects only proteins with a strong predicted | |
| 5 signal peptide, and then runs TMHMM v2.0 on those, and selects only | |
| 6 proteins without a predicted trans-membrane helix. This workflow was | |
| 7 used in Kikuchi et al (2001), and is a simplification of the candidate | |
| 8 effector protocol described in Jones et al (2009). | |
| 1 | 9 |
| 3 | 10 See http://www.galaxyproject.org for information about the Galaxy Project. |
| 11 | |
| 1 | 12 |
| 3 | 13 References |
| 14 ========== | |
| 15 | |
| 16 Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, et al. (2011) | |
| 17 Genomic insights into the origin of parasitism in the emerging plant | |
| 18 pathogen Bursaphelenchus xylophilus. PLoS Pathog 7: e1002219. | |
| 1 | 19 http://dx.doi.org/10.1371/journal.ppat.1002219 |
| 20 | |
| 3 | 21 Jones JT, Kumar A, Pylypenko LA, Thirugnanasambandam A, et al. (2009) |
| 22 Identification and functional characterization of effectors in expressed | |
| 23 sequence tags from various life cycle stages of the potato cyst nematode | |
| 24 Globodera pallida. Mol Plant Pathol 10: 815–28. | |
| 1 | 25 http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x |
| 26 | |
| 3 | 27 Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) |
| 28 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95. | |
| 1 | 29 http://dx.doi.org/10.1016/j.jmb.2004.05.028 |
| 30 | |
| 3 | 31 Krogh A, Larsson B, von Heijne G, Sonnhammer E (2001) |
| 32 Predicting transmembrane protein topology with a hidden Markov model: | |
| 33 application to complete genomes. J Mol Biol 305: 567- 580. | |
| 1 | 34 http://dx.doi.org/10.1006/jmbi.2000.4315 |
| 35 | |
| 36 | |
| 37 Availability | |
| 38 ============ | |
| 39 | |
| 3 | 40 This workflow is available to download and/or install from the main |
| 41 Galaxy Tool Shed: | |
| 42 | |
| 1 | 43 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow |
| 44 | |
| 3 | 45 Test releases (which should not normally be used) are on the Test Tool Shed: |
| 46 | |
| 47 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow | |
| 48 | |
| 1 | 49 Development is being done on github here: |
| 3 | 50 |
| 1 | 51 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow |
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aecb871dfe4c
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52 |
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aecb871dfe4c
Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
peterjc
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53 |
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aecb871dfe4c
Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
peterjc
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54 Dependencies |
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aecb871dfe4c
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55 ============ |
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aecb871dfe4c
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peterjc
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56 |
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aecb871dfe4c
Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
peterjc
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57 These dependencies should be resolved automatically via the Galaxy Tool Shed: |
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aecb871dfe4c
Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
peterjc
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58 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp |
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aecb871dfe4c
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59 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id |
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aecb871dfe4c
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60 |
| 3 | 61 However, at the time of writing those Galaxy tools have their own |
| 62 dependencies required for this workflow which require manual | |
| 63 installation (SignalP v3.0 and TMHMM v2.0). | |
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64 |
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65 |
| 3 | 66 Developers |
| 67 ========== | |
| 68 | |
| 69 This workflow is under source code control here: | |
| 70 | |
| 71 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/secreted_protein_workflow | |
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aecb871dfe4c
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peterjc
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72 |
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Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
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73 To prepare the tar-ball for uploading to the Tool Shed, I use this: |
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aecb871dfe4c
Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
peterjc
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74 |
| 3 | 75 $ tar -cf secreted_protein_workflow.tar.gz README.txt repository_dependencies.xml secreted_protein_workflow.ga |
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aecb871dfe4c
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peterjc
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76 |
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aecb871dfe4c
Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
peterjc
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77 Check this, |
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aecb871dfe4c
Uploaded v0.0.1b, repository_dependencies.xml with implicit current toolshed & latest revision
peterjc
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78 |
| 3 | 79 $ tar -tzf secreted_protein_workflow.tar.gz |
| 80 README.txt | |
| 81 repository_dependencies.xml | |
| 82 secreted_protein_workflow.ga |