Mercurial > repos > iuc > meme_fimo

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
author iuc
date Sat, 27 Nov 2021 09:44:17 +0000
parents 0c5239d1aa65
children c5209f38700d
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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">
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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 color="#000000">
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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 <td bgcolor="#FFDD00"><a href="fimo.tsv""><b>Results in TSV Format</b></a></td>
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21 <td bgcolor="#FFDDFF"><a href="fimo.gff""><b>Results in GFF3 Format</b></a></td>
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22 </tr>
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23 </table>
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24 <center><big><b>FIMO - Motif search tool</b></big></center>
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25 FIMO version 5.0.5, (Release date: Mon Mar 18 20:12:19 2019 -0700)
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26 For further information on how to interpret these results please access <a href="http://meme-suite.org/doc/fimo-output-format.html">http://meme-suite.org/doc/fimo-output-format.html</a>.<br>
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27 To get a copy of the FIMO software please access <a href="http://meme-suite.org">http://meme-suite.org</a>
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28 <p>If you use FIMO in your research, please cite the following paper:<br>
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29 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
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30 "FIMO: Scanning for occurrences of a given motif",
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31 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
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32 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
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33 Database contains 1 sequences, 16569 residues
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34 <table>
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35 <thead>
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36 </thead>
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37 <tbody>
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38 </tbody>
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39 </table>
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40 A 0.278 C 0.222 G 0.222 T 0.278 </p>
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41 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
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42 There were 11 motif occurences with a p-value less than 0.0001.
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43 The full set of motif occurences can be seen in the
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44 TSV (tab-delimited values) output file
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45 the GFF3 file
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46 which may be suitable for uploading to the
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47 (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
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48 or the XML file
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49 The <i>p</i>-value of a motif occurrence is defined as the
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50 probability of a random sequence of the same length as the motif
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51 matching that position of the sequence with as good or better a score.
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52 The score for the match of a position in a sequence to a motif
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53 is computed by summing the appropriate entries from each column of
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54 the position-dependent scoring matrix that represents the motif.
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55 The q-value of a motif occurrence is defined as the
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56 false discovery rate if the occurrence is accepted as significant.
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57 <li>The table is sorted by increasing <i>p</i>-value.</li>
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58 <th>Motif ID</th>
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59 <th>Alt ID</th>
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60 <th>Sequence Name</th>
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61 <th>Strand</th>
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62 <th>Start</th>
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63 <th>End</th>
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64 <th>p-value</th>
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65 <th>q-value</th>
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66 <th>Matched Sequence</th>
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67 <tr>
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68 <td style="text-align:left;">CCAGCAY</td>
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69 <td style="text-align:left;">DREME-5</td>
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70 <td style="text-align:left;">chrM</td>
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71 <td style="text-align:center;">+</td>
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72 <td style="text-align:left;">510</td>
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73 <td style="text-align:left;">516</td>
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74 <td style="text-align:left;">4.15e-05</td>
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75 <td style="text-align:left;">0.683</td>
13
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76 <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
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77 <td style="text-align:left;">2093</td>
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78 <td style="text-align:left;">2099</td>
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79 <td style="text-align:left;">8.2e-05</td>
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80 <td style="text-align:left;">0.332</td>
13
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81 <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
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82 </tr>
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83 <hr>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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84 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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85 Command line:
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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86 Settings:
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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87 This information can be useful in the event you wish to report a
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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88 problem with the FIMO software.
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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89 </body>
4eb02864e5df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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90 </html>