Mercurial > repos > peterjc > secreted_protein_workflow

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author peterjc
date Fri, 09 Nov 2018 11:16:44 -0500
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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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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. (2011), and is a simplification of
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8 the candidate effector protocol described in Jones et al. (2009).
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10 See http://www.galaxyproject.org for information about the Galaxy Project.
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13 Availability
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14 ============
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16 This workflow is available to download and/or install from the main
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17 Galaxy Tool Shed:
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19 http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
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21 Test releases (which should not normally be used) are on the Test Tool Shed:
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23 http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
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25 Development is being done on github here:
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27 https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow
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30 Sample Data
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31 ===========
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33 This workflow was developed and run on several nematode species. For example,
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34 try the protein set for *Bursaphelenchus xylophilus* (Kikuchi et al. 2011):
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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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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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40 18,074 sequences. The expected result (selecting organism type Eukaryote)
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41 is a FASTA protein file of 2,297 predicted secreted protein sequences.
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44 Citation
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45 ========
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47 If you use this workflow directly, or a derivative of it, in work leading
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48 to a scientific publication, please cite:
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50 Cock, P.J.A. and Pritchard, L. (2014). Galaxy as a platform for identifying
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51 candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
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52 Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds.
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53 Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7.
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54 http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7
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56 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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57 Galaxy tools and workflows for sequence analysis with applications
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58 in molecular plant pathology. PeerJ 1:e167
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59 https://doi.org/10.7717/peerj.167
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61 Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
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62 Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
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63 https://doi.org/10.1016/j.jmb.2004.05.028
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65 Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001)
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66 Predicting transmembrane protein topology with a hidden Markov model:
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67 application to complete genomes. J Mol Biol 305: 567- 580.
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68 https://doi.org/10.1006/jmbi.2000.4315
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71 Additional References
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72 =====================
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74 Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011)
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75 Genomic insights into the origin of parasitism in the emerging plant
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76 pathogen *Bursaphelenchus xylophilus*. PLoS Pathog 7: e1002219.
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77 https://doi.org/10.1371/journal.ppat.1002219
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79 Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)
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80 Identification and functional characterization of effectors in expressed
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81 sequence tags from various life cycle stages of the potato cyst nematode
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82 *Globodera pallida*. Mol Plant Pathol 10: 815–28.
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83 https://doi.org/10.1111/j.1364-3703.2009.00585.x
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86 Dependencies
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87 ============
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89 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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91 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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92 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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93
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94 However, at the time of writing those Galaxy tools have their own
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95 dependencies required for this workflow which require manual
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96 installation (SignalP v3.0 and TMHMM v2.0).
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97
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98
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99 History
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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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104 ------- ----------------------------------------------------------------------
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105 v0.0.1 - Initial release to Tool Shed (May, 2013)
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106 - Expanded README file to include example data
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107 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
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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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110 is a README file with sample data, and a requested citation.
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111 v0.0.3 - Use MIT licence.
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112 ======= ======================================================================
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113
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114
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115 Developers
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116 ==========
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117
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118 This workflow is under source code control here:
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119
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120 https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow
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121
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122 To prepare the tar-ball for uploading to the Tool Shed, I use this:
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123
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124 $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga
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125
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126 Check this,
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127
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128 $ tar -tzf secreted_protein_workflow.tar.gz
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129 README.rst
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130 repository_dependencies.xml
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131 secreted_protein_workflow.ga
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132
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133
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134 Licence (MIT)
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135 =============
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136
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137 Permission is hereby granted, free of charge, to any person obtaining a copy
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138 of this software and associated documentation files (the "Software"), to deal
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139 in the Software without restriction, including without limitation the rights
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140 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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141 copies of the Software, and to permit persons to whom the Software is
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142 furnished to do so, subject to the following conditions:
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143
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144 The above copyright notice and this permission notice shall be included in
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145 all copies or substantial portions of the Software.
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146
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147 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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148 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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149 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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150 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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151 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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152 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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153 THE SOFTWARE.