0
|
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="4.7.0" release="0 EST 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 --verbosity 1 AATAAA.motif /Users/xuebing/Downloads/hotair-target.fa.fasta</command-line>
|
|
9 <settings>
|
|
10 <setting name="output directory">fimo_out</setting>
|
|
11 <setting name="MEME file name">AATAAA.motif</setting>
|
|
12 <setting name="sequence file name">/Users/xuebing/Downloads/hotair-target.fa.fasta</setting>
|
|
13 <setting name="background file name">(null)</setting>
|
|
14 <setting name="motif name">motif</setting>
|
|
15 <setting name="allow clobber">true</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">true</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="832" num-residues="573269" />
|
|
28 <alphabet>nucleotide</alphabet>
|
|
29 <motif name="AATAAA" width="6" best-possible-match="AATAAA"/>
|
|
30 <motif name="AATAAA" width="6" best-possible-match="TTTATT"/>
|
|
31 <background source="non-redundant database">
|
|
32 <value letter="A">0.275</value>
|
|
33 <value letter="C">0.225</value>
|
|
34 <value letter="G">0.225</value>
|
|
35 <value letter="T">0.275</value>
|
|
36 </background>
|
|
37 <cisml-file>cisml.xml</cisml-file>
|
|
38 </fimo>
|