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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:11:27 -0400
parents
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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">
+<meta 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 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)
+</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.
+<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></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 hsa_chrM.fa
+  <br />
+  Database contains 1 sequences, 16569 residues
+</p>
+<p>
+  MOTIFS dreme_fimo_input_1.xml (DNA)
+  <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;text-align:left;" >
+         BEST POSSIBLE MATCH
+        </th>
+      </tr>
+    </thead>
+    <tbody>
+      <tr>
+        <td style="text-align:right;">ACTAAYH</td>
+        <td style="text-align:right;padding-left: 1em;">7</td>
+        <td style="text-align:left;padding-left: 1em;">ACTAACA</td>
+       </tr>
+      <tr>
+        <td style="text-align:right;">YTAACA</td>
+        <td style="text-align:right;padding-left: 1em;">6</td>
+        <td style="text-align:left;padding-left: 1em;">TTAACA</td>
+       </tr>
+      <tr>
+        <td style="text-align:right;">TCTGT</td>
+        <td style="text-align:right;padding-left: 1em;">5</td>
+        <td style="text-align:left;padding-left: 1em;">TCTGT</td>
+       </tr>
+      <tr>
+        <td style="text-align:right;">SCCAGG</td>
+        <td style="text-align:right;padding-left: 1em;">6</td>
+        <td style="text-align:left;padding-left: 1em;">CCCAGG</td>
+       </tr>
+      <tr>
+        <td style="text-align:right;">CCAGCAY</td>
+        <td style="text-align:right;padding-left: 1em;">7</td>
+        <td style="text-align:left;padding-left: 1em;">CCAGCAC</td>
+       </tr>
+      <tr>
+        <td style="text-align:right;">GMATGT</td>
+        <td style="text-align:right;padding-left: 1em;">6</td>
+        <td style="text-align:left;padding-left: 1em;">GAATGT</td>
+       </tr>
+    </tbody>
+  </table>
+</p>
+<p>
+Random model letter frequencies (fimo_background_probs_hsa_chrM.txt):
+<br/>
+
+A 0.278 C 0.222 G 0.222 T 0.278 </p>
+</div>
+<hr>
+<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
+<hr>
+<ul>
+<li>
+There were 11 motif occurences with a p-value less than 0.0001.
+
+The full set of motif occurences can be seen in the
+tab-delimited plain text output file
+<a href="fimo.txt">fimo.txt</a>, 
+the GFF file 
+<a href="fimo.gff">fimo.gff</a> 
+which may be suitable for uploading to the 
+<a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
+(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
+or the XML file 
+<a href="fimo.xml">fimo.xml</a>.
+</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 q-value of a motif occurrence is defined as the
+false discovery rate if the occurrence is accepted as significant.
+</li>
+<li>The table is sorted by increasing p-value.</li>
+</ul>
+<table border="1">
+<thead>
+<tr>
+<th>Motif ID</th>
+<th>Alt ID</th>
+<th>Sequence Name</th>
+<th>Strand</th>
+<th>Start</th>
+<th>End</th>
+<th>p-value</th>
+<th>q-value</th>
+<th>Matched Sequence</th>
+</tr>
+</thead>
+<tbody>
+    <tr>
+      <td style="text-align:left;">CCAGCAY</td>
+      <td style="text-align:left;">DREME-5</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">510</td>
+      <td style="text-align:left;">516</td>
+      <td style="text-align:left;">4.15e-05</td>
+      <td style="text-align:left;">0.668</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">CCAGCAY</td>
+      <td style="text-align:left;">DREME-5</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">5137</td>
+      <td style="text-align:left;">5143</td>
+      <td style="text-align:left;">4.15e-05</td>
+      <td style="text-align:left;">0.668</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAC</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">440</td>
+      <td style="text-align:left;">446</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">-</td>
+      <td style="text-align:left;">2093</td>
+      <td style="text-align:left;">2099</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">-</td>
+      <td style="text-align:left;">2299</td>
+      <td style="text-align:left;">2305</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">5186</td>
+      <td style="text-align:left;">5192</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">6530</td>
+      <td style="text-align:left;">6536</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">7742</td>
+      <td style="text-align:left;">7748</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">13657</td>
+      <td style="text-align:left;">13663</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">ACTAAYH</td>
+      <td style="text-align:left;">DREME-1</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">13741</td>
+      <td style="text-align:left;">13747</td>
+      <td style="text-align:left;">8.2e-05</td>
+      <td style="text-align:left;">0.327</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">ACTAACA</td>
+   </tr>
+    <tr>
+      <td style="text-align:left;">CCAGCAY</td>
+      <td style="text-align:left;">DREME-5</td>
+      <td style="text-align:left;">chrM</td>
+      <td style="text-align:center;">+</td>
+      <td style="text-align:left;">4241</td>
+      <td style="text-align:left;">4247</td>
+      <td style="text-align:left;">9.37e-05</td>
+      <td style="text-align:left;">1</td>
+      <td style="text-align:left;font-size:x-large;font-family:monospace;">CCAGCAT</td>
+   </tr>
+</tbody>
+</table>
+
+<hr>
+<center><big><b><a name="debugging_information">DEBUGGING INFORMATION</a></b></big></center>
+<hr>
+<p>
+Command line:
+</p>
+<pre>
+fimo -oc fimo_test2_out --bgfile fimo_background_probs_hsa_chrM.txt dreme_fimo_input_1.xml hsa_chrM.fa
+</pre>
+<p>
+Settings:
+</p>
+<pre>
+<table>
+  <tr>
+    <td style="padding-right: 2em">output_directory = fimo_test2_out</td>
+    <td style="padding-left: 5em; padding-right: 2em">MEME file name = dreme_fimo_input_1.xml</td>
+    <td style="padding-left: 5em; padding-right: 2em">sequence file name = hsa_chrM.fa</td>
+  </tr>  <tr>
+    <td style="padding-right: 2em">background file name = fimo_background_probs_hsa_chrM.txt</td>
+    <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td>
+    <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td>
+  </tr>  <tr>
+    <td style="padding-right: 2em">allow clobber = true</td>
+    <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td>
+    <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = 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 strand = false</td>
+  </tr>
+  <tr>
+    <td style="padding-right: 2em">threshold type = p-value</td>
+    <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td>
+    <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td>
+  </tr>
+  <tr>
+    <td style="padding-right: 2em">alpha = 1</td>
+    <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td>
+    <td style="padding-left: 5em; padding-right: 2em"></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>