|
11
|
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>
|
