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view test-data/dreme_output_test1.xml @ 2:3e5c80594237 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
author iuc
date Wed, 11 Dec 2019 18:04:55 -0500
parents cb8a2242bf03
children f33d77dcacce
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<dreme version="5.0.5" release="Mon Mar 18 20:12:19 2019 -0700">
  <model>
    <negatives name="shuffled positive sequences" count="1000" from="shuffled"/>
    <alphabet name="RNA" like="rna">
      <letter id="A" symbol="A" name="Adenine" colour="CC0000"/>
      <letter id="C" symbol="C" name="Cytosine" colour="0000CC"/>
      <letter id="G" symbol="G" name="Guanine" colour="FFB300"/>
      <letter id="U" symbol="U" aliases="T" name="Uracil" colour="008000"/>
      <letter id="N" symbol="N" aliases="X." equals="ACGU" name="Any base"/>
      <letter id="V" symbol="V" equals="ACG" name="Not U"/>
      <letter id="H" symbol="H" equals="ACU" name="Not G"/>
      <letter id="D" symbol="D" equals="AGU" name="Not C"/>
      <letter id="B" symbol="B" equals="CGU" name="Not A"/>
      <letter id="M" symbol="M" equals="AC" name="Amino"/>
      <letter id="R" symbol="R" equals="AG" name="Purine"/>
      <letter id="W" symbol="W" equals="AU" name="Weak"/>
      <letter id="S" symbol="S" equals="CG" name="Strong"/>
      <letter id="Y" symbol="Y" equals="CU" name="Pyrimidine"/>
      <letter id="K" symbol="K" equals="GU" name="Keto"/>
    </alphabet>
    <strands>none</strands>
    <background A="0.221" C="0.245" G="0.221" U="0.312" from="dataset"/>
    <stop evalue="0.05"/>
    <ngen>100</ngen>
    <add_pv_thresh>0.01</add_pv_thresh>
    <seed>1</seed>
  </model>
  <motifs>
    <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="1.2e-013" unerased_evalue="1.2e-013">
      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
      <pos A="0.000000" C="0.294118" G="0.000000" U="0.705882"/>
      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
      <pos A="0.000000" C="1.000000" G="0.000000" U="0.000000"/>
      <pos A="0.000000" C="0.474946" G="0.000000" U="0.525054"/>
      <match seq="UUUUCC" p="147" n="75" pvalue="1.8e-007" evalue="8.1e-003"/>
      <match seq="UUUUCU" p="155" n="94" pvalue="2.2e-005" evalue="1.0e+000"/>
      <match seq="UUCUCU" p="94" n="51" pvalue="1.3e-004" evalue="6.1e+000"/>
      <match seq="UUCUCC" p="75" n="42" pvalue="1.1e-003" evalue="5.0e+001"/>
    </motif>
    <motif id="m02" alt="DREME-2" seq="YAGG" length="4" nsites="793" p="600" n="416" pvalue="1.1e-016" evalue="5.1e-012" unerased_evalue="2.4e-012">
      <pos A="0.000000" C="0.692308" G="0.000000" U="0.307692"/>
      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
      <match seq="CAGG" p="441" n="304" pvalue="1.5e-010" evalue="6.6e-006"/>
      <match seq="UAGG" p="232" n="165" pvalue="1.1e-004" evalue="4.7e+000"/>
    </motif>
    <motif id="m03" alt="DREME-3" seq="GAAGAW" length="6" nsites="89" p="81" n="22" pvalue="8.2e-010" evalue="3.4e-005" unerased_evalue="3.5e-004">
      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
      <pos A="0.494382" C="0.000000" G="0.000000" U="0.505618"/>
      <match seq="GAAGAU" p="45" n="7" pvalue="2.4e-008" evalue="9.9e-004"/>
      <match seq="GAAGAA" p="40" n="16" pvalue="7.9e-004" evalue="3.3e+001"/>
    </motif>
    <motif id="m04" alt="DREME-4" seq="SMUGGA" length="6" nsites="119" p="110" n="47" pvalue="9.1e-008" evalue="3.7e-003" unerased_evalue="2.6e-005">
      <pos A="0.000000" C="0.529412" G="0.470588" U="0.000000"/>
      <pos A="0.428571" C="0.571429" G="0.000000" U="0.000000"/>
      <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/>
      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
      <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/>
      <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/>
      <match seq="GAUGGA" p="22" n="6" pvalue="1.7e-003" evalue="7.1e+001"/>
      <match seq="GCUGGA" p="33" n="14" pvalue="3.6e-003" evalue="1.5e+002"/>
      <match seq="CCUGGA" p="32" n="15" pvalue="8.6e-003" evalue="3.5e+002"/>
      <match seq="CAUGGA" p="29" n="13" pvalue="9.1e-003" evalue="3.7e+002"/>
    </motif>
  </motifs>
</dreme>