Mercurial > repos > yhoogstrate > segmentation_fold

annotate test-data/segments_truncated.xml @ 26:660c25c66c8a draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa
author erasmus-medical-center
date Fri, 24 Feb 2017 04:18:08 -0500
parents 59ab674be4b5
children
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3
59ab674be4b5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <root>
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3 <segments>
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4 <segment>
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5 <id>Kt-CD-box.UGU</id><!-- Common -->
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6 <sequence_5prime>UGUGAU</sequence_5prime>
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7 <bonds > :::</bonds>
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8 <sequence_3prime> AGU</sequence_3prime>
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9 <energy>-11.1072</energy>
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10 <directions>
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11 <five_prime>true</five_prime>
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12 <three_prime>true</three_prime>
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13 </directions>
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14 </segment>
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15
59ab674be4b5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty
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16 <segment>
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17 <id>Kt-CD-box.CGU</id><!-- Common -->
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18 <sequence_5prime>CGUGAU</sequence_5prime>
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19 <bonds > :::</bonds>
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20 <sequence_3prime> AGU</sequence_3prime>
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21 <energy>-11.1072</energy>
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22 <directions>
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23 <five_prime>true</five_prime>
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24 <three_prime>true</three_prime>
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25 </directions>
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26 </segment>
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27 </segments>
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28
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29
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30 <segmentloops />
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31
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32
59ab674be4b5 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4b12ac5efae0802d2614747a639475d8778a68b4-dirty
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33 <!-- RNA-Molecules -->
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34 <rnas>
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35 <rna>
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36 <title>C/D-box snoRNA</title>
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37 <organism>A. fulgidus</organism>
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38 <sequence>GCUCUGACCGAAAGGCGUGAUGAGC</sequence>
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39
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40 <structures>
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41 <structure>
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42 <associated_segments>
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43 <link>Kt-CD-box.CGU</link>
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44 </associated_segments>
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45 <dot_bracket type="full" >(((((((((....))...)))))))</dot_bracket>
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46 </structure>
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47
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48 <structure>
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49 <associated_segments />
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50 <dot_bracket />
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51 </structure>
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52 </structures>
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53
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54 <references>
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55 <pdb>1RLG</pdb>
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56 <url>http://www.sciencedirect.com/science/article/pii/S0969212604001169</url>
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57 </references>
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58 </rna>
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59
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60 <rna>
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61 <title>Artificial double C/D K-turn construct</title>
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62 <sequence>GGGAGUCUUGUGAUGAGAAGUACUGGAUCUGAAGUAGCCCUUUUUGGGCUACUUGUGAUGAAACACUCAUGGUCUGAAGACUCCC</sequence>
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63
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64 <structures>
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65 <structure>
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66 <associated_segments>
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67 <link>Kt-CD-box.UGU</link>
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68 </associated_segments>
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69 <dot_bracket type="full" >((((((((...((((?????????????((((((((((((.....))))))))...))))?????????????))))))))))))</dot_bracket>
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70 </structure>
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71
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72 <structure>
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73 <associated_segments />
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74 <dot_bracket />
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75 </structure>
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76 </structures>
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77
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78 <references>
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79 <pdb>3ICX</pdb>
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80 <pdb>3ID6</pdb>
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81 <doi>http://dx.doi.org/10.1038/nature09688</doi>
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82 </references>
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83 </rna>
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84 </rnas>
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85 </root>