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comparison tools/protein_analysis/rxlr_motifs.xml @ 32:20da7f48b56f draft

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author peterjc
date Thu, 17 Jun 2021 08:19:32 +0000
parents 6d9d7cdf00fc
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31:3c9bbbc6cbbe 32:20da7f48b56f
1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.14"> 1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.15">
2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description> 2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
3 <requirements> 3 <requirements>
4 <!-- Need SignalP for all the models --> 4 <!-- Need SignalP for all the models -->
5 <requirement type="package">signalp</requirement> 5 <requirement type="package">signalp</requirement>
6 <!-- Need HMMER for Whisson et al. (2007) --> 6 <!-- Need HMMER for Whisson et al. (2007) -->
136 cite Cock et al. (2013) and the appropriate method paper(s): 136 cite Cock et al. (2013) and the appropriate method paper(s):
137 137
138 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). 138 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
139 Galaxy tools and workflows for sequence analysis with applications 139 Galaxy tools and workflows for sequence analysis with applications
140 in molecular plant pathology. PeerJ 1:e167 140 in molecular plant pathology. PeerJ 1:e167
141 http://dx.doi.org/10.7717/peerj.167 141 https://doi.org/10.7717/peerj.167
142 142
143 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). 143 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).
144 A translocation signal for delivery of oomycete effector proteins into host plant cells. 144 A translocation signal for delivery of oomycete effector proteins into host plant cells.
145 Nature 450:115-118. 145 Nature 450:115-118.
146 http://dx.doi.org/10.1038/nature06203 146 https://doi.org/10.1038/nature06203
147 147
148 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun (2007). 148 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun (2007).
149 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. 149 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes.
150 The Plant Cell 19:2349-2369. 150 The Plant Cell 19:2349-2369.
151 http://dx.doi.org/10.1105/tpc.107.051037 151 https://doi.org/10.1105/tpc.107.051037
152 152
153 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar (2006). 153 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar (2006).
154 The malarial host-targeting signal is conserved in the Irish potato famine pathogen. 154 The malarial host-targeting signal is conserved in the Irish potato famine pathogen.
155 PLoS Pathogens, 2(5):e50. 155 PLoS Pathogens, 2(5):e50.
156 http://dx.doi.org/10.1371/journal.ppat.0020050 156 https://doi.org/10.1371/journal.ppat.0020050
157 157
158 Trudy A. Torto, Shuang Li, Allison Styer, Edgar Huitema, Antonino Testa, Neil A.R. Gow, Pieter van West and Sophien Kamoun (2003). 158 Trudy A. Torto, Shuang Li, Allison Styer, Edgar Huitema, Antonino Testa, Neil A.R. Gow, Pieter van West and Sophien Kamoun (2003).
159 EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen *phytophthora*. 159 EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen *phytophthora*.
160 Genome Research, 13:1675-1685. 160 Genome Research, 13:1675-1685.
161 http://dx.doi.org/10.1101/gr.910003 161 https://doi.org/10.1101/gr.910003
162 162
163 Sean R. Eddy (1998). 163 Sean R. Eddy (1998).
164 Profile hidden Markov models. 164 Profile hidden Markov models.
165 Bioinformatics, 14(9):755–763. 165 Bioinformatics, 14(9):755–763.
166 http://dx.doi.org/10.1093/bioinformatics/14.9.755 166 https://doi.org/10.1093/bioinformatics/14.9.755
167 167
168 Nielsen, Engelbrecht, Brunak and von Heijne (1997). 168 Nielsen, Engelbrecht, Brunak and von Heijne (1997).
169 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. 169 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
170 Protein Engineering, 10:1-6. 170 Protein Engineering, 10:1-6.
171 http://dx.doi.org/10.1093/protein/10.1.1 171 https://doi.org/10.1093/protein/10.1.1
172 172
173 This wrapper is available to install into other Galaxy Instances via the Galaxy 173 This wrapper is available to install into other Galaxy Instances via the Galaxy
174 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 174 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
175 </help> 175 </help>
176 <citations> 176 <citations>