Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/rxlr_motifs.xml @ 16:7de64c8b258d draft
Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
author | peterjc |
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date | Wed, 18 Sep 2013 06:16:58 -0400 |
parents | e52220a9ddad |
children | e6cc27d182a8 |
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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> |