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date Fri, 09 Mar 2012 19:37:19 -0500
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1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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">
3 <head>
4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
5 <title>FIMO Results</title>
6 <style type="text/css">
7 td.left {text-align: left;}
8 td.right {text-align: right; padding-right: 1cm;}
9 </style>
10 </head>
11 <body bgcolor="#D5F0FF">
12 <a name="top_buttons"></a><hr>
13 <table summary="buttons" align="left" cellspacing="0"><tr>
14 <td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
15 <td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
16 <td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
17 </tr></table>
18 <br><br><hr>
19 <center><big><b>FIMO - Motif search tool</b></big></center>
20 <hr>
21 <p>
22 FIMO version 4.7.0,
23 (Release date: 0 EST 20)
24 </p>
25 <p>
26 For further information on how to interpret these results
27 or to get a copy of the FIMO software please access
28 <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
29 <p>If you use FIMO in your research, please cite the following paper:<br>
30 Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
31 "FIMO: Scanning for occurrences of a given motif",
32 <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
33 </p>
34 <hr>
35 <center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
36 <hr>
37 <div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
38 <p>
39 DATABASE
40 /Users/xuebing/Downloads/hotair-target.fa.fasta<br>
41 Database contains
42 832
43 sequences,
44 573269
45 residues
46 </p>
47 <p>
48 MOTIFS
49 AATAAA.motif
50 (nucleotide)
51 <table>
52 <thead><tr>
53 <th style="border-bottom: 1px dashed;">MOTIF</th>
54 <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
55 <th style="border-bottom: 1px dashed; padding-left: 1em;" align="left">
56 BEST POSSIBLE MATCH
57 </th>
58 </tr></thead>
59 <tbody>
60 <tr>
61 <td align="right">AATAAA</td>
62 <td align="right" style="padding-left: 1em;">6</td>
63 <td align="left" style="padding-left: 1em;">AATAAA</td>
64 </tr>
65 <tr>
66 <td align="right">AATAAA</td>
67 <td align="right" style="padding-left: 1em;">6</td>
68 <td align="left" style="padding-left: 1em;">TTTATT</td>
69 </tr>
70 </tbody>
71 </table></p>
72 <p>
73 Random model letter frequencies
74 (from non-redundant database):
75 <br>A 0.275 C 0.225 G 0.225 T 0.275 </p>
76 </div>
77 <hr>
78 <center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
79 <hr>
80 <ul>
81 <li> Each of the following
82 0
83 motif occurrences has
84
85 p-value less than
86 0.0001</li>
87 <li> The p-value of a motif occurrence is defined as the
88 probability of a random sequence of the same length as the motif
89 matching that position of the sequence with as good or better a score.
90 </li>
91 <li> The score for the match of a position in a sequence to a motif
92 is computed by summing the appropriate entries from each column of
93 the position-dependent scoring matrix that represents the motif.
94 </li>
95 <li>The table is sorted by increasing p-value.</li>
96 <li>If the start position is larger than the end position,
97 the motif occurrence is on the reverse strand.
98 </li>
99 </ul>
100 <table border="1">
101 <thead><tr>
102 <th>Motif</th>
103 <th>Sequence Name</th>
104 <th>Strand</th>
105 <th>Start</th>
106 <th>End</th>
107 <th>p-value</th>
108 <th>Matched Sequence</th>
109 </tr></thead>
110 <tbody></tbody>
111 </table>
112 <hr>
113 <center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
114 <hr>
115 <p>
116 Command line:
117 </p>
118 <pre>fimo --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta</pre>
119 <p>
120 Settings:
121 </p>
122 <pre><table>
123 <tr>
124 <td style="padding-right: 2em">output directory = fimo_out</td>
125 <td style="padding-left: 5em; padding-right: 2em">MEME file name = AATAAA.motif</td>
126 <td style="padding-left: 5em; padding-right: 2em">sequence file name = /Users/xuebing/Downloads/hotair-target.fa.fasta</td>
127 </tr>
128 <tr>
129 <td style="padding-right: 2em">background file name = (null)</td>
130 <td style="padding-left: 5em; padding-right: 2em">motif name = motif</td>
131 <td style="padding-left: 5em; padding-right: 2em">allow clobber = true</td>
132 </tr>
133 <tr>
134 <td style="padding-right: 2em">compute q-values = true</td>
135 <td style="padding-left: 5em; padding-right: 2em">output p-threshold set = false</td>
136 <td style="padding-left: 5em; padding-right: 2em">output q-threshold set = false</td>
137 </tr>
138 <tr>
139 <td style="padding-right: 2em">text only = false</td>
140 <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
141 <td style="padding-left: 5em; padding-right: 2em">max sequence length = 250000000</td>
142 </tr>
143 <tr>
144 <td style="padding-right: 2em">output q-value threshold = 1</td>
145 <td style="padding-left: 5em; padding-right: 2em">output p-value threshold = 0.0001</td>
146 <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
147 </tr>
148 <tr>
149 <td style="padding-right: 2em">verbosity = 1</td>
150 <td style="padding-left: 5em; padding-right: 2em"></td>
151 <td align="right"></td>
152 </tr>
153 </table></pre>
154 <p>
155 This information can be useful in the event you wish to report a
156 problem with the FIMO software.
157 </p>
158 <hr>
159 <span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
160 </body>
161 </html>