comparison test-data/dreme_output_test1.xml @ 5:f33d77dcacce draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"

4:e383d4bc8682

<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"/>

      <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>

5:f33d77dcacce

  <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"/>

      <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>