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annotate README.txt @ 0:e21be67dbc91 draft

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author peterjc
date Mon, 06 May 2013 13:58:44 -0400
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1 This Tool Shed Repository contains a workflow for comparing three RXLR prediction methods with a Venn Diagram, and creates a FASTA file of any proteins passing all three methods.
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4 References
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5 ==========
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7 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard and Paul R. J. Birch A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450:115-118, 2007.
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8 http://dx.doi.org/10.1038/nature06203
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10 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun. Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007.
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11 http://dx.doi.org/10.1105/tpc.107.051037
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13 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar. The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathogens, 2(5):e50, 2006.
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14 http://dx.doi.org/10.1371/journal.ppat.0020050
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17 Availability
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18 ============
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19
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20 This workflow is available on the main Galaxy Tool Shed:
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21 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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23 Development is being done on github here:
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24 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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27 Dependencies
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28 ============
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30 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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31 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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32 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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33 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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34
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35 However, at the time of writing those Galaxy tools have their own dependencies
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36 required for this workflow which require manual installation (SignalP v3.0,
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37 HMMER v2.0, and the R/Bioconductor package limma).