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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 <title>FIMO Results</title>
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6 <style type="text/css">
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7 td.left {text-align: left;}
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8 td.right {text-align: right; padding-right: 1cm;}
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9 </style>
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10 </head>
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11 <body bgcolor="#D5F0FF">
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12 <a name="top_buttons"></a><hr>
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13 <table summary="buttons" align="left" cellspacing="0"><tr>
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14 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
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15 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
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16 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
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17 </tr></table>
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18 <br><br><hr>
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19 <center><big><b>FIMO - Motif search tool</b></big></center>
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20 <hr>
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21 <p>
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22 FIMO version 4.7.0,
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23 (Release date: 0 EST 20)
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24 </p>
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25 <p>
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26 For further information on how to interpret these results
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27 or to get a copy of the FIMO software please access
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28 <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
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29 <p>If you use FIMO in your research, please cite the following paper:<br>
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30 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
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31 "FIMO: Scanning for occurrences of a given motif",
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32 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
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33 </p>
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34 <hr>
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35 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
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36 <hr>
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37 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
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38 <p>
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39 DATABASE
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40 /Users/xuebing/Downloads/hotair-target.fa.fasta<br>
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41 Database contains
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42 832
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43 sequences,
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44 573269
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45 residues
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46 </p>
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47 <p>
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48 MOTIFS
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49 AATAAA.motif
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50 (nucleotide)
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51 <table>
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52 <thead><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;" align="left">
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56 BEST POSSIBLE MATCH
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57 </th>
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58 </tr></thead>
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59 <tbody>
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60 <tr>
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61 <td align="right">AATAAA</td>
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62 <td align="right" style="padding-left: 1em;">6</td>
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63 <td align="left" style="padding-left: 1em;">AATAAA</td>
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64 </tr>
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65 <tr>
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66 <td align="right">AATAAA</td>
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67 <td align="right" style="padding-left: 1em;">6</td>
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68 <td align="left" style="padding-left: 1em;">TTTATT</td>
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69 </tr>
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70 </tbody>
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71 </table></p>
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72 <p>
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73 Random model letter frequencies
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74 (from non-redundant database):
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75 <br>A 0.275 C 0.225 G 0.225 T 0.275 </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> Each of the following
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82 0
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83 motif occurrences has
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84
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85 p-value less than
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86 0.0001</li>
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87 <li> The p-value of a motif occurrence is defined as the
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88 probability of a random sequence of the same length as the motif
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89 matching that position of the sequence with as good or better a score.
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90 </li>
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91 <li> The score for the match of a position in a sequence to a motif
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92 is computed by summing the appropriate entries from each column of
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93 the position-dependent scoring matrix that represents the motif.
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94 </li>
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95 <li>The table is sorted by increasing p-value.</li>
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96 <li>If the start position is larger than the end position,
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97 the motif occurrence is on the reverse strand.
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98 </li>
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99 </ul>
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100 <table border="1">
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101 <thead><tr>
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102 <th>Motif</th>
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103 <th>Sequence Name</th>
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104 <th>Strand</th>
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105 <th>Start</th>
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106 <th>End</th>
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107 <th>p-value</th>
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108 <th>Matched Sequence</th>
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109 </tr></thead>
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110 <tbody></tbody>
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111 </table>
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112 <hr>
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113 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
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114 <hr>
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115 <p>
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116 Command line:
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117 </p>
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118 <pre>fimo --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta</pre>
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119 <p>
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120 Settings:
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121 </p>
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122 <pre><table>
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123 <tr>
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124 <td style="padding-right: 2em">output directory = fimo_out</td>
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125 <td style="padding-left: 5em; padding-right: 2em">MEME file name = AATAAA.motif</td>
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126 <td style="padding-left: 5em; padding-right: 2em">sequence file name = /Users/xuebing/Downloads/hotair-target.fa.fasta</td>
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127 </tr>
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128 <tr>
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129 <td style="padding-right: 2em">background file name = (null)</td>
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130 <td style="padding-left: 5em; padding-right: 2em">motif name = motif</td>
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131 <td style="padding-left: 5em; padding-right: 2em">allow clobber = true</td>
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132 </tr>
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133 <tr>
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134 <td style="padding-right: 2em">compute q-values = true</td>
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135 <td style="padding-left: 5em; padding-right: 2em">output p-threshold set = false</td>
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136 <td style="padding-left: 5em; padding-right: 2em">output q-threshold set = false</td>
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137 </tr>
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138 <tr>
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139 <td style="padding-right: 2em">text only = false</td>
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140 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
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141 <td style="padding-left: 5em; padding-right: 2em">max sequence length = 250000000</td>
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142 </tr>
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143 <tr>
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144 <td style="padding-right: 2em">output q-value threshold = 1</td>
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145 <td style="padding-left: 5em; padding-right: 2em">output p-value threshold = 0.0001</td>
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146 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
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147 </tr>
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148 <tr>
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149 <td style="padding-right: 2em">verbosity = 1</td>
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150 <td style="padding-left: 5em; padding-right: 2em"></td>
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151 <td align="right"></td>
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152 </tr>
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153 </table></pre>
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154 <p>
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155 This information can be useful in the event you wish to report a
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156 problem with the FIMO software.
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157 </p>
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158 <hr>
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159 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
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160 </body>
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161 </html>
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