Mercurial > repos > iuc > meme_fimo

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<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>
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<center><big><b>FIMO - Motif search tool</b></big></center>
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<p>
FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
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<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>
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<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
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  DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat
  <br />
  Database contains 1 sequences, 5386 residues
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<p>
  MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein)
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        <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
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        <td style="text-align:right;">1</td>
        <td style="text-align:right;padding-left: 1em;">11</td>
        <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td>
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<p>
Random model letter frequencies (from non-redundant database):
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A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
W 0.013 Y 0.033 </p>
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<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
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<li>
There were 1937 motif occurences with a p-value less than 0.0001.
<b>Only the most significant 1000 matches are shown here.</b>

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>
author	iuc
date	Tue, 08 Mar 2016 08:10:52 -0500
parents	fd522a964017
children	eca84de658b0