Mercurial > repos > iuc > meme_fimo

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit d84a6599817ce37c2548cc98b6a01beb7fe4020a
author iuc
date Wed, 20 Jan 2016 08:46:01 -0500
parents fd522a964017
children eca84de658b0
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fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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2 <html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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3 <head>
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4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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5 <meta charset="UTF-8">
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6 <title>FIMO Results</title>
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7 <style type="text/css">
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8 td.left {text-align: left;}
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9 td.right {text-align: right; padding-right: 1cm;}
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10 </style>
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11 </head>
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12 <body bgcolor="#D5F0FF">
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13 <a name="top_buttons"></a>
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14 <hr>
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15 <table summary="buttons" align="left" cellspacing="0">
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16 <tr>
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17 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
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18 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
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19 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
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20 </tr>
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21 </table>
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22 <br/>
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23 <br/>
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24 <hr/>
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25 <center><big><b>FIMO - Motif search tool</b></big></center>
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26 <hr>
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27 <p>
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28 FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
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29 </p>
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30 <p>
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31 For further information on how to interpret these results
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32 or to get a copy of the FIMO software please access
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33 <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
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34 <p>If you use FIMO in your research, please cite the following paper:<br>
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35 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
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36 "FIMO: Scanning for occurrences of a given motif",
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37 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
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38 <a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>
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39 <hr>
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40 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
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41 <hr>
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42 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
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43 <p>
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44 DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat
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45 <br />
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46 Database contains 1 sequences, 5386 residues
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47 </p>
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48 <p>
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49 MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein)
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50 <table>
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51 <thead>
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52 <tr>
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53 <th style="border-bottom: 1px dashed;">MOTIF</th>
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54 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
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55 <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
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56 BEST POSSIBLE MATCH
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57 </th>
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58 </tr>
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59 </thead>
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60 <tbody>
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61 <tr>
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62 <td style="text-align:right;">1</td>
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63 <td style="text-align:right;padding-left: 1em;">11</td>
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64 <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td>
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65 </tr>
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66 </tbody>
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67 </table>
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68 </p>
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69 <p>
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70 Random model letter frequencies (from non-redundant database):
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71 <br/>
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72
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73 A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
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74 L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
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75 W 0.013 Y 0.033 </p>
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76 </div>
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77 <hr>
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78 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
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79 <hr>
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80 <ul>
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81 <li>
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82 There were 1937 motif occurences with a p-value less than 0.0001.
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83 <b>Only the most significant 1000 matches are shown here.</b>
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84
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85 The full set of motif occurences can be seen in the
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86 tab-delimited plain text output file
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87 <a href="fimo.txt">fimo.txt</a>,
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88 the GFF file
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89 <a href="fimo.gff">fimo.gff</a>
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90 which may be suitable for uploading to the
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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91 <a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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92 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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93 or the XML file
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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94 <a href="fimo.xml">fimo.xml</a>.
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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95 </li>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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96 <li>
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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97 The p-value of a motif occurrence is defined as the
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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98 probability of a random sequence of the same length as the motif
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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99 matching that position of the sequence with as good or better a score.
fd522a964017 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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100 </li>