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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <!-- Begin document body -->
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3 <fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
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4 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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5 xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
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6 >
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7 <command-line>fimo --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line>
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8 <settings>
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9 <setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files</setting>
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10 <setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting>
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11 <setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting>
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12 <setting name="allow clobber">false</setting>
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13 <setting name="compute q-values">true</setting>
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14 <setting name="parse genomic coord.">false</setting>
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15 <setting name="text only">false</setting>
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16 <setting name="scan both strands">false</setting>
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17 <setting name="output threshold">0.0001</setting>
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18 <setting name="threshold type">p-value</setting>
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19 <setting name="max stored scores">100000</setting>
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20 <setting name="pseudocount">0.1</setting>
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21 <setting name="verbosity">1</setting>
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22 </settings>
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23 <sequence-data num-sequences="1" num-residues="5386" />
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24 <alphabet name="Protein" like="protein">
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25 <letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
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26 <letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
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27 <letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
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28 <letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
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29 <letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
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30 <letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
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31 <letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
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32 <letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
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33 <letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
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34 <letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
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35 <letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
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36 <letter id="N" symbol="N" name="Asparagine" colour="008000"/>
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37 <letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
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38 <letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
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39 <letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
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40 <letter id="S" symbol="S" name="Serine" colour="008000"/>
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41 <letter id="T" symbol="T" name="Threonine" colour="008000"/>
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42 <letter id="V" symbol="V" name="Valine" colour="0000CC"/>
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43 <letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
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44 <letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
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45 <letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
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46 <letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
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47 <letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
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48 <letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
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49 </alphabet>
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50 <motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
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51 <background source="non-redundant database">
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52 <value letter="A">0.073</value>
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53 <value letter="C">0.018</value>
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54 <value letter="D">0.052</value>
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55 <value letter="E">0.062</value>
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56 <value letter="F">0.040</value>
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57 <value letter="G">0.069</value>
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58 <value letter="H">0.022</value>
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59 <value letter="I">0.056</value>
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60 <value letter="K">0.058</value>
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61 <value letter="L">0.092</value>
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62 <value letter="M">0.023</value>
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63 <value letter="N">0.046</value>
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64 <value letter="P">0.051</value>
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65 <value letter="Q">0.041</value>
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66 <value letter="R">0.052</value>
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67 <value letter="S">0.074</value>
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68 <value letter="T">0.059</value>
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69 <value letter="V">0.064</value>
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70 <value letter="W">0.013</value>
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71 <value letter="Y">0.033</value>
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72 </background>
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73 <cisml-file>cisml.xml</cisml-file>
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74 </fimo>
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