Mercurial > repos > jjkoehorst > sapp

comparison rnaseq/cutadapt/test-data/meme/fimo/fimo_output_xml_1.xml @ 11:a712b378e090

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cutadapt added
author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 16:33:42 +0100
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10:3378d12591ea 11:a712b378e090
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <?xml-stylesheet type="text/xsl" href="fimo-to-html.xsl"?>
3 <!-- Begin document body -->
4 <fimo version="4.6.0" release="8 PST 20">
5 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
6 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
7 >
8 <command-line>fimo --o /path/to/dataset_?_files --verbosity 1 /path/to/dataset_?.dat /path/to/dataset_?.dat</command-line>
9 <settings>
10 <setting name="output directory">/path/to/dataset_?_files</setting>
11 <setting name="MEME file name">/path/to/dataset_?.dat</setting>
12 <setting name="sequence file name">/path/to/dataset_?.dat</setting>
13 <setting name="background file name">(null)</setting>
14 <setting name="motif name">motif</setting>
15 <setting name="allow clobber">false</setting>
16 <setting name="compute q-values">true</setting>
17 <setting name="output p-threshold set">false</setting>
18 <setting name="output q-threshold set">false</setting>
19 <setting name="text only">false</setting>
20 <setting name="scan both strands">false</setting>
21 <setting name="max sequence length">250000000</setting>
22 <setting name="output q-value threshold"> 1</setting>
23 <setting name="output p-value threshold">0.0001</setting>
24 <setting name="pseudocount">0.1</setting>
25 <setting name="verbosity">1</setting>
26 </settings>
27 <sequence-data num-sequences="1" num-residues="5386" />
28 <alphabet>protein</alphabet>
29 <motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
30 <background source="non-redundant database">
31 <value letter="A">0.073</value>
32 <value letter="C">0.018</value>
33 <value letter="D">0.052</value>
34 <value letter="E">0.062</value>
35 <value letter="F">0.040</value>
36 <value letter="G">0.069</value>
37 <value letter="H">0.022</value>
38 <value letter="I">0.056</value>
39 <value letter="K">0.058</value>
40 <value letter="L">0.092</value>
41 <value letter="M">0.023</value>
42 <value letter="N">0.046</value>
43 <value letter="P">0.051</value>
44 <value letter="Q">0.041</value>
45 <value letter="R">0.052</value>
46 <value letter="S">0.074</value>
47 <value letter="T">0.059</value>
48 <value letter="V">0.064</value>
49 <value letter="W">0.013</value>
50 <value letter="Y">0.033</value>
51 </background>
52 <cisml-file>cisml.xml</cisml-file>
53 </fimo>