Mercurial > repos > jjkoehorst > sapp
view rnaseq/cutadapt/test-data/meme/fimo/fimo_output_xml_1.xml @ 11:a712b378e090
cutadapt added
author | jjkoehorst <jasperkoehorst@gmail.com> |
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date | Sat, 21 Feb 2015 16:33:42 +0100 |
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<?xml version="1.0" encoding="UTF-8" standalone="no"?> <?xml-stylesheet type="text/xsl" href="fimo-to-html.xsl"?> <!-- Begin document body --> <fimo version="4.6.0" release="8 PST 20"> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" > <command-line>fimo --o /path/to/dataset_?_files --verbosity 1 /path/to/dataset_?.dat /path/to/dataset_?.dat</command-line> <settings> <setting name="output directory">/path/to/dataset_?_files</setting> <setting name="MEME file name">/path/to/dataset_?.dat</setting> <setting name="sequence file name">/path/to/dataset_?.dat</setting> <setting name="background file name">(null)</setting> <setting name="motif name">motif</setting> <setting name="allow clobber">false</setting> <setting name="compute q-values">true</setting> <setting name="output p-threshold set">false</setting> <setting name="output q-threshold set">false</setting> <setting name="text only">false</setting> <setting name="scan both strands">false</setting> <setting name="max sequence length">250000000</setting> <setting name="output q-value threshold"> 1</setting> <setting name="output p-value threshold">0.0001</setting> <setting name="pseudocount">0.1</setting> <setting name="verbosity">1</setting> </settings> <sequence-data num-sequences="1" num-residues="5386" /> <alphabet>protein</alphabet> <motif name="1" width="11" best-possible-match="GGGGTATAAAA"/> <background source="non-redundant database"> <value letter="A">0.073</value> <value letter="C">0.018</value> <value letter="D">0.052</value> <value letter="E">0.062</value> <value letter="F">0.040</value> <value letter="G">0.069</value> <value letter="H">0.022</value> <value letter="I">0.056</value> <value letter="K">0.058</value> <value letter="L">0.092</value> <value letter="M">0.023</value> <value letter="N">0.046</value> <value letter="P">0.051</value> <value letter="Q">0.041</value> <value letter="R">0.052</value> <value letter="S">0.074</value> <value letter="T">0.059</value> <value letter="V">0.064</value> <value letter="W">0.013</value> <value letter="Y">0.033</value> </background> <cisml-file>cisml.xml</cisml-file> </fimo>