Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/signalp3.xml @ 20:a538e182fab3 draft

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Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
author peterjc
date Tue, 10 Sep 2013 08:55:19 -0400
parents 4cd848c5590b
children 90e3d02f8013
comparison
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19:4cd848c5590b 20:a538e182fab3
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167 Signal peptides are found at the start of a protein, so there is limited value in providing the full length sequence, and providing the full sequence slows down the analysis. Furthermore, SignalP has an upper bound on the sequence length it will accept (6000bp). Thus for practical reasons it is useful to truncate the proteins before passing them to SignalP. However, the precise point they are truncated does have a small influence on some score values, and thus to the results. 167 Signal peptides are found at the start of a protein, so there is limited value in providing the full length sequence, and providing the full sequence slows down the analysis. Furthermore, SignalP has an upper bound on the sequence length it will accept (6000bp). Thus for practical reasons it is useful to truncate the proteins before passing them to SignalP. However, the precise point they are truncated does have a small influence on some score values, and thus to the results.
168 168
169 **References** 169 **References**
170 170
171 Bendtsen, Nielsen, von Heijne, and Brunak. 171 If you use this Galaxy tool in work leading to a scientific publication please
172 cite the following papers:
173
174 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
175 Galaxy tools and workflows for sequence analysis with applications
176 in molecular plant pathology. PeerJ 1:e167
177 http://dx.doi.org/10.7717/peerj.167
178
179 Bendtsen, Nielsen, von Heijne, and Brunak (2004).
172 Improved prediction of signal peptides: SignalP 3.0. 180 Improved prediction of signal peptides: SignalP 3.0.
173 J. Mol. Biol., 340:783-795, 2004. 181 J. Mol. Biol., 340:783-795.
174 http://dx.doi.org/10.1016/j.jmb.2004.05.028 182 http://dx.doi.org/10.1016/j.jmb.2004.05.028
175 183
176 Nielsen, Engelbrecht, Brunak and von Heijne. 184 Nielsen, Engelbrecht, Brunak and von Heijne (1997).
177 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. 185 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
178 Protein Engineering, 10:1-6, 1997. 186 Protein Engineering, 10:1-6.
179 http://dx.doi.org/10.1093/protein/10.1.1 187 http://dx.doi.org/10.1093/protein/10.1.1
180 188
181 Nielsen and Krogh. 189 Nielsen and Krogh (1998).
182 Prediction of signal peptides and signal anchors by a hidden Markov model. 190 Prediction of signal peptides and signal anchors by a hidden Markov model.
183 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6), 191 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6),
184 AAAI Press, Menlo Park, California, pp. 122-130, 1998. 192 AAAI Press, Menlo Park, California, pp. 122-130.
185 http://www.ncbi.nlm.nih.gov/pubmed/9783217 193 http://www.ncbi.nlm.nih.gov/pubmed/9783217
186 194
187 http://www.cbs.dtu.dk/services/SignalP-3.0/output.php 195 See also http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
188 196
189 This wrapper is available to install into other Galaxy Instances via the Galaxy 197 This wrapper is available to install into other Galaxy Instances via the Galaxy
190 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 198 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
191 </help> 199 </help>
192 </tool> 200 </tool>