Mercurial > repos > iuc > meme_fimo
diff test-data/fimo_output_test1.html @ 13:4eb02864e5df draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
| author | iuc |
|---|---|
| date | Thu, 17 May 2018 14:11:00 -0400 |
| parents | |
| children | 0c5239d1aa65 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_test1.html Thu May 17 14:11:00 2018 -0400 @@ -0,0 +1,300 @@ +<!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 meme_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;">TACTAAYM</td> + <td style="text-align:right;padding-left: 1em;">8</td> + <td style="text-align:left;padding-left: 1em;">TACTAACA</td> + </tr> + </tbody> + </table> +</p> +<p> +Random model letter frequencies (--nrdb--): +<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> +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;">TACTAAYM</td> + <td style="text-align:left;">MEME-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;">2306</td> + <td style="text-align:left;">2.18e-05</td> + <td style="text-align:left;">0.142</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">6529</td> + <td style="text-align:left;">6536</td> + <td style="text-align:left;">2.18e-05</td> + <td style="text-align:left;">0.142</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">7741</td> + <td style="text-align:left;">7748</td> + <td style="text-align:left;">2.18e-05</td> + <td style="text-align:left;">0.142</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">13656</td> + <td style="text-align:left;">13663</td> + <td style="text-align:left;">2.18e-05</td> + <td style="text-align:left;">0.142</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">13740</td> + <td style="text-align:left;">13747</td> + <td style="text-align:left;">2.18e-05</td> + <td style="text-align:left;">0.142</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">861</td> + <td style="text-align:left;">868</td> + <td style="text-align:left;">3.96e-05</td> + <td style="text-align:left;">0.185</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">9346</td> + <td style="text-align:left;">9353</td> + <td style="text-align:left;">3.96e-05</td> + <td style="text-align:left;">0.185</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACC</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">3767</td> + <td style="text-align:left;">3774</td> + <td style="text-align:left;">6.62e-05</td> + <td style="text-align:left;">0.216</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">5497</td> + <td style="text-align:left;">5504</td> + <td style="text-align:left;">6.62e-05</td> + <td style="text-align:left;">0.216</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">10105</td> + <td style="text-align:left;">10112</td> + <td style="text-align:left;">6.62e-05</td> + <td style="text-align:left;">0.216</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAATA</td> + </tr> + <tr> + <td style="text-align:left;">TACTAAYM</td> + <td style="text-align:left;">MEME-1</td> + <td style="text-align:left;">chrM</td> + <td style="text-align:center;">+</td> + <td style="text-align:left;">10959</td> + <td style="text-align:left;">10966</td> + <td style="text-align:left;">8.79e-05</td> + <td style="text-align:left;">0.261</td> + <td style="text-align:left;font-size:x-large;font-family:monospace;">TACTAACT</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_test1_out meme_fimo_input_1.xml hsa_chrM.fa +</pre> +<p> +Settings: +</p> +<pre> +<table> + <tr> + <td style="padding-right: 2em">output_directory = fimo_test1_out</td> + <td style="padding-left: 5em; padding-right: 2em">MEME file name = meme_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 = --nrdb--</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>