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comparison tools/protein_analysis/rxlr_motifs.xml @ 16:7de64c8b258d draft

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Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:16:58 -0400
parents e52220a9ddad
children e6cc27d182a8
comparison
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15:6abd809cefdd 16:7de64c8b258d
1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.6"> 1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.7">
2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description> 2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 rxlr_motifs.py $fasta_file 8 $model $tabular_file 4 rxlr_motifs.py $fasta_file 8 $model $tabular_file
5 ##I want the number of threads to be a Galaxy config option... 5 ##I want the number of threads to be a Galaxy config option...
6 </command> 6 </command>
30 <test> 30 <test>
31 <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta" /> 31 <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta" />
32 <param name="model" value="Win2007" /> 32 <param name="model" value="Win2007" />
33 <output name="tabular_file" file="rxlr_win_et_al_2007.tabular" ftype="tabular" /> 33 <output name="tabular_file" file="rxlr_win_et_al_2007.tabular" ftype="tabular" />
34 </test> 34 </test>
35 <test>
36 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
37 <param name="model" value="Bhattacharjee2006"/>
38 <output name="tabular_file" file="empty_rxlr.Bhattacharjee2006.tabular" ftype="tabular"/>
39 </test>
40 <test>
41 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
42 <param name="model" value="Win2007"/>
43 <output name="tabular_file" file="empty_rxlr.Win2007.tabular" ftype="tabular"/>
44 </test>
45 <test>
46 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
47 <param name="model" value="Whisson2007"/>
48 <output name="tabular_file" file="empty_rxlr.Whisson2007.tabular" ftype="tabular"/>
49 </test>
35 </tests> 50 </tests>
36 <help> 51 <help>
37 52
38 **Background** 53 **Background**
39 54
57 **Bhattacharjee et al. (2006) RXLR Model** 72 **Bhattacharjee et al. (2006) RXLR Model**
58 73
59 Looks for the oomycete motif RXLR as described in Bhattacharjee et al. (2006). 74 Looks for the oomycete motif RXLR as described in Bhattacharjee et al. (2006).
60 75
61 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9, 76 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
62 a SignalP Neural Network (NN) predicted clevage site giving a signal peptide 77 a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
63 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be 78 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
64 after but within 100 amino acids of the clevage site. 79 after but within 100 amino acids of the cleavage site.
65 SignalP is run truncating the sequences to the first 70 amino acids, which was 80 SignalP is run truncating the sequences to the first 70 amino acids, which was
66 the default on the SignalP webservice used in Bhattacharjee et al. (2006). 81 the default on the SignalP webservice used in Bhattacharjee et al. (2006).
67 82
68 83
69 **Win et al. (2007) RXLR Model** 84 **Win et al. (2007) RXLR Model**
70 85
71 Looks for the protein motif RXLR as described in Win et al. (2007). 86 Looks for the protein motif RXLR as described in Win et al. (2007).
72 87
73 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9, 88 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
74 a SignalP Neural Network (NN) predicted clevage site giving a signal peptide 89 a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
75 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be 90 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
76 after the clevage site and start between amino acids 30 and 60. 91 after the cleavage site and start between amino acids 30 and 60.
77 SignalP is run truncating the sequences to the first 70 amino acids, to match 92 SignalP is run truncating the sequences to the first 70 amino acids, to match
78 the methodology of Torto et al. (2003) followed in Win et al. (2007). 93 the methodology of Torto et al. (2003) followed in Win et al. (2007).
79 94
80 95
81 **Whisson et al. (2007) RXLR-EER with HMM** 96 **Whisson et al. (2007) RXLR-EER with HMM**
118 133
119 ----- 134 -----
120 135
121 **References** 136 **References**
122 137
123 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 138 If you use this Galaxy tool in work leading to a scientific publication please
139 cite Cock et al. (2013) and the appropriate method paper(s):
140
141 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
142 Galaxy tools and workflows for sequence analysis with applications
143 in molecular plant pathology. PeerJ 1:e167
144 http://dx.doi.org/10.7717/peerj.167
145
146 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 (2007).
124 A translocation signal for delivery of oomycete effector proteins into host plant cells. 147 A translocation signal for delivery of oomycete effector proteins into host plant cells.
125 Nature 450:115-118, 2007. 148 Nature 450:115-118.
126 http://dx.doi.org/10.1038/nature06203 149 http://dx.doi.org/10.1038/nature06203
127 150
128 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun. 151 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun (2007).
129 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. 152 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes.
130 The Plant Cell 19:2349-2369, 2007. 153 The Plant Cell 19:2349-2369.
131 http://dx.doi.org/10.1105/tpc.107.051037 154 http://dx.doi.org/10.1105/tpc.107.051037
132 155
133 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar. 156 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar (2006).
134 The malarial host-targeting signal is conserved in the Irish potato famine pathogen. 157 The malarial host-targeting signal is conserved in the Irish potato famine pathogen.
135 PLoS Pathogens, 2(5):e50, 2006. 158 PLoS Pathogens, 2(5):e50.
136 http://dx.doi.org/10.1371/journal.ppat.0020050 159 http://dx.doi.org/10.1371/journal.ppat.0020050
137 160
138 Trudy A. Torto, Shuang Li, Allison Styer, Edgar Huitema, Antonino Testa, Neil A.R. Gow, Pieter van West and Sophien Kamoun. 161 Trudy A. Torto, Shuang Li, Allison Styer, Edgar Huitema, Antonino Testa, Neil A.R. Gow, Pieter van West and Sophien Kamoun (2003).
139 EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen *phytophthora*. 162 EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen *phytophthora*.
140 Genome Research, 13:1675-1685, 2003. 163 Genome Research, 13:1675-1685.
141 http://dx.doi.org/10.1101/gr.910003 164 http://dx.doi.org/10.1101/gr.910003
142 165
143 Sean R. Eddy. 166 Sean R. Eddy (1998).
144 Profile hidden Markov models. 167 Profile hidden Markov models.
145 Bioinformatics, 14(9):755–763, 1998 168 Bioinformatics, 14(9):755–763.
146 http://dx.doi.org/10.1093/bioinformatics/14.9.755 169 http://dx.doi.org/10.1093/bioinformatics/14.9.755
147 170
148 Nielsen, Engelbrecht, Brunak and von Heijne. 171 Nielsen, Engelbrecht, Brunak and von Heijne (1997).
149 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. 172 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
150 Protein Engineering, 10:1-6, 1997. 173 Protein Engineering, 10:1-6.
151 http://dx.doi.org/10.1093/protein/10.1.1 174 http://dx.doi.org/10.1093/protein/10.1.1
152 175
176 This wrapper is available to install into other Galaxy Instances via the Galaxy
177 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
153 </help> 178 </help>
154 </tool> 179 </tool>