Mercurial > repos > iuc > meme_dreme
diff test-data/fimo_output_html_1.html @ 0:b386032d758d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author | iuc |
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date | Wed, 25 Apr 2018 12:13:22 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_html_1.html Wed Apr 25 12:13:22 2018 -0400 @@ -0,0 +1,97 @@ +<!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> +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> + <br /> + Database contains 1 sequences, 5386 residues +</p> +<p> + <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;">1</td> + <td style="text-align:right;padding-left: 1em;">11</td> + <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td> + </tr> + </tbody> + </table> +</p> +<p> +Random model letter frequencies (from non-redundant database): +<br/> + +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> +</div> +<hr> +<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center> +<hr> +<ul> +<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> +<li> +The score for the match of a position in a sequence to a motif