Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/signalp3.xml @ 6:a290c6d4e658
Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 18:07:09 -0400 |
| parents | 81caef04ce8b |
| children | 9b45a8743100 |
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| 5:0f1c61998b22 | 6:a290c6d4e658 |
|---|---|
| 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.7"> | 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.8"> |
| 2 <description>Find signal peptides in protein sequences</description> | 2 <description>Find signal peptides in protein sequences</description> |
| 3 <command interpreter="python"> | 3 <command interpreter="python"> |
| 4 signalp3.py $organism $truncate 8 $fasta_file $tabular_file | 4 signalp3.py $organism $truncate 8 $fasta_file $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> |
| 122 **References** | 122 **References** |
| 123 | 123 |
| 124 Bendtsen, Nielsen, von Heijne, and Brunak. | 124 Bendtsen, Nielsen, von Heijne, and Brunak. |
| 125 Improved prediction of signal peptides: SignalP 3.0. | 125 Improved prediction of signal peptides: SignalP 3.0. |
| 126 J. Mol. Biol., 340:783-795, 2004. | 126 J. Mol. Biol., 340:783-795, 2004. |
| 127 http://dx.doi.org/10.1016/j.jmb.2004.05.028 | |
| 127 | 128 |
| 128 Nielsen, Engelbrecht, Brunak and von Heijne. | 129 Nielsen, Engelbrecht, Brunak and von Heijne. |
| 129 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. | 130 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. |
| 130 Protein Engineering, 10:1-6, 1997. | 131 Protein Engineering, 10:1-6, 1997. |
| 132 http://dx.doi.org/10.1093/protein/10.1.1 | |
| 131 | 133 |
| 132 Nielsen and Krogh. | 134 Nielsen and Krogh. |
| 133 Prediction of signal peptides and signal anchors by a hidden Markov model. | 135 Prediction of signal peptides and signal anchors by a hidden Markov model. |
| 134 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6), | 136 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6), |
| 135 AAAI Press, Menlo Park, California, pp. 122-130, 1998. | 137 AAAI Press, Menlo Park, California, pp. 122-130, 1998. |
| 138 http://www.ncbi.nlm.nih.gov/pubmed/9783217 | |
| 136 | 139 |
| 137 http://www.cbs.dtu.dk/services/SignalP-3.0/output.php | 140 http://www.cbs.dtu.dk/services/SignalP-3.0/output.php |
| 138 | 141 |
| 139 </help> | 142 </help> |
| 140 </tool> | 143 </tool> |