Mercurial > repos > xuebing > sharplabtool

diff tools/mytools/fimo_out/fimo.html @ 0:9071e359b9a3
Uploaded
author: xuebing
date: Fri, 09 Mar 2012 19:37:19 -0500
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+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<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">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>FIMO Results</title>
+<style type="text/css">
+        td.left {text-align: left;}
+        td.right {text-align: right; padding-right: 1cm;}
+      </style>
+</head>
+<body bgcolor="#D5F0FF">
+<a name="top_buttons"></a><hr>
+<table summary="buttons" align="left" cellspacing="0"><tr>
+<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
+<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
+<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
+</tr></table>
+<br><br><hr>
+<center><big><b>FIMO - Motif search tool</b></big></center>
+<hr>
+<p>
+      FIMO version 4.7.0, 
+      (Release date: 0 EST 20)
+    </p>
+<p>
+      For further information on how to interpret these results
+      or to get a copy of the FIMO software please access
+      <a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
+<p>If you use FIMO in your research, please cite the following paper:<br>
+      Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
+      "FIMO: Scanning for occurrences of a given motif",
+      <i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
+    </p>
+<hr>
+<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
+<hr>
+<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
+<p>
+        DATABASE 
+        /Users/xuebing/Downloads/hotair-target.fa.fasta<br>
+        Database contains 
+        832
+        sequences,
+        573269
+        residues
+      </p>
+<p>
+        MOTIFS 
+        AATAAA.motif 
+        (nucleotide)
+        <table>
+<thead><tr>
+<th style="border-bottom: 1px dashed;">MOTIF</th>
+<th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
+<th style="border-bottom: 1px dashed; padding-left: 1em;" align="left">
+              BEST POSSIBLE MATCH
+            </th>
+</tr></thead>
+<tbody>
+<tr>
+<td align="right">AATAAA</td>
+<td align="right" style="padding-left: 1em;">6</td>
+<td align="left" style="padding-left: 1em;">AATAAA</td>
+</tr>
+<tr>
+<td align="right">AATAAA</td>
+<td align="right" style="padding-left: 1em;">6</td>
+<td align="left" style="padding-left: 1em;">TTTATT</td>
+</tr>
+</tbody>
+</table></p>
+<p>
+        Random model letter frequencies 
+        (from non-redundant database):
+        <br>A 0.275 C 0.225 G 0.225 T 0.275 </p>
+</div>
+<hr>
+<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
+<hr>
+<ul>
+<li> Each of the following 
+    0
+    motif occurrences has 
+    
+        p-value less than 
+        0.0001</li>
+<li> The p-value of a motif occurrence is defined as the
+    probability of a random sequence of the same length as the motif
+    matching that position of the sequence with as good or better a score.
+    </li>
+<li> The score for the match of a position in a sequence to a motif
+    is computed by summing the appropriate entries from each column of
+    the position-dependent scoring matrix that represents the motif.
+    </li>
+<li>The table is sorted by increasing p-value.</li>
+<li>If the start position is larger than the end position,
+    the motif occurrence is on the reverse strand.
+    </li>
+</ul>
+<table border="1">
+<thead><tr>
+<th>Motif</th>
+<th>Sequence Name</th>
+<th>Strand</th>
+<th>Start</th>
+<th>End</th>
+<th>p-value</th>
+<th>Matched Sequence</th>
+</tr></thead>
+<tbody></tbody>
+</table>
+<hr>
+<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
+<hr>
+<p>
+    Command line:
+    </p>
+<pre>fimo --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta</pre>
+<p>
+    Settings:
+    </p>
+<pre><table>
+<tr>
+<td style="padding-right: 2em">output directory = fimo_out</td>
+<td style="padding-left: 5em; padding-right: 2em">MEME file name = AATAAA.motif</td>
+<td style="padding-left: 5em; padding-right: 2em">sequence file name = /Users/xuebing/Downloads/hotair-target.fa.fasta</td>
+</tr>
+<tr>
+<td style="padding-right: 2em">background file name = (null)</td>
+<td style="padding-left: 5em; padding-right: 2em">motif name = motif</td>
+<td style="padding-left: 5em; padding-right: 2em">allow clobber = true</td>
+</tr>
+<tr>
+<td style="padding-right: 2em">compute q-values = true</td>
+<td style="padding-left: 5em; padding-right: 2em">output p-threshold set = false</td>
+<td style="padding-left: 5em; padding-right: 2em">output q-threshold set = false</td>
+</tr>
+<tr>
+<td style="padding-right: 2em">text only = false</td>
+<td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td>
+<td style="padding-left: 5em; padding-right: 2em">max sequence length = 250000000</td>
+</tr>
+<tr>
+<td style="padding-right: 2em">output q-value threshold =   1</td>
+<td style="padding-left: 5em; padding-right: 2em">output p-value threshold = 0.0001</td>
+<td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
+</tr>
+<tr>
+<td style="padding-right: 2em">verbosity = 1</td>
+<td style="padding-left: 5em; padding-right: 2em"></td>
+<td align="right"></td>
+</tr>
+</table></pre>
+<p>
+      This information can be useful in the event you wish to report a
+      problem with the FIMO software.
+    </p>
+<hr>
+<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span>
+</body>
+</html>
author	xuebing
date	Fri, 09 Mar 2012 19:37:19 -0500
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