<?xml version="1.0"?>

<!DOCTYPE rnaml SYSTEM "http://www-lbit.iro.umontreal.ca/rnaml/current/rnaml.dtd">
<rnaml comment="Example output file for mFold" version="1.1">
  <!-- First sequence and its associated models ******************* --> 
  <molecule id="seq1">
    <sequence>
      <seq-data>
	  GCGGAUUUAG CUCAGUUGGG AGAGCGCCAG ACUGAAGAUC UGGAGGUCCU GUGUUCGAUC
          CACAGAAUUC GCACCA
	</seq-data>
    </sequence>
    <structure>
      <!-- Start of model 1 for sequence 1 ********************** -->
      <model analysis-ids="mFold" id="mod1.1">
        <model-info>
          <method>mFold</method>
          <free-energy analysis-ids="refined">-19.400000</free-energy>
          <free-energy analysis-ids="initial">-20.299999</free-energy>
        </model-info>
        <base>
          <position>1</position>
          <base-type>G</base-type>
        </base>
        <base>
          <position>72</position>
          <base-type>C</base-type>
        </base>
        <str-annotation>
          <base-pair>
            <base-id-5p>
              <base-id>
                <position>1</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>72</position>
              </base-id>
            </base-id-3p>
          </base-pair>
        </str-annotation>
      </model>
      <!-- End of model 1 for sequence 1 ************************ -->

      <!-- Start of model 2 for sequence 1 ********************** -->
      <model analysis-ids="mFold" id="mod1.2">
        <model-info>
          <method>mFold</method>
          <free-energy>-19.400000</free-energy>
        </model-info>
        <base>
          <position>1</position>
          <base-type>G</base-type>
        </base>
        <base>
          <position>2</position>
          <base-type>C</base-type>
        </base>
        <str-annotation>
          <base-pair>
            <base-id-5p>
              <base-id>
                <position>1</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>72</position>
              </base-id>
            </base-id-3p>
          </base-pair>
        </str-annotation>
      </model>
      <!-- End of model 2 for sequence 1 ************************ -->
    </structure>
  </molecule>

  <!-- Second sequence and its associated models ******************* --> 
  <molecule id="seq2">
    <sequence circular="true">
      <seq-data>
	  GCGGAUUUAG CUCAGUUGGG AGAGCGCCAG ACUGAAGAUC UGGAGGUCCU GUGUUCGAUC
          CACAGAAUUC GCACCA
	</seq-data>
    </sequence>
    <structure>
      <!-- Start of model 2 for sequence 2 ********************** -->
      <model analysis-ids="mFold" id="mod2.1">
        <model-info>
          <method>mFold</method>
          <free-energy>-21.799999</free-energy>
        </model-info>
        <base>
          <position>1</position>
          <base-type>G</base-type>
        </base>
        <base>
          <position>72</position>
          <base-type>C</base-type>
        </base>
        <str-annotation>
          <base-pair>
            <base-id-5p>
              <base-id>
                <position>1</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>72</position>
              </base-id>
            </base-id-3p>
          </base-pair>
        </str-annotation>
      </model>
      <!-- End of model 1 for sequence 2 ************************ -->
      
      <!-- Start of model 2 for sequence 2 ********************** -->
      <model analysis-ids="mFold" id="mod2.2">
        <model-info>
          <method>mFold</method>
          <free-energy>-19.400000</free-energy>
        </model-info>
        <base>
          <position>1</position>
          <base-type>G</base-type>
        </base>
        <base>
          <position>2</position>
          <base-type>C</base-type>
        </base>
        <str-annotation>
          <base-pair>
            <base-id-5p>
              <base-id>
                <position>1</position>
              </base-id>
            </base-id-5p>
            <base-id-3p>
              <base-id>
                <position>72</position>
              </base-id>
            </base-id-3p>
          </base-pair>
        </str-annotation>
      </model>
      <!-- End of model 2 for sequence 2 ************************ -->
    </structure>
  </molecule>
  
  <!-- Information about the analysis ***************************** -->
  <analysis reference-ids="mathews1999" id="mFold">
    <program>
      <prog-name>mFold</prog-name>
      <prog-version>3.0.1</prog-version>
    </program>
    <date>
      <day>8</day>
      <month>3</month>
      <year>2002</year>
    </date>
    <author>
      <person>
        <first-name>Patrick</first-name>
        <last-name>Gendron</last-name>
      </person>
    </author>
  </analysis>
  <analysis id="refined">
    <program>
      <prog-name>Name of the program</prog-name>
    </program>
  </analysis>
  <analysis id="initial">
    <program>
      <prog-name>Name of the program</prog-name>
    </program>
  </analysis>
  <reference id="mathews1999">
    <author>
      <person>
        <first-name>D.H.</first-name>
        <last-name>Mathews</last-name>
      </person>
    </author>
    <author>
      <person>
        <first-name>J.</first-name>
        <last-name>Sabina</last-name>
      </person>
    </author>
    <author>
      <person>
        <first-name>M.</first-name>
        <last-name>Zuker</last-name>
      </person>
    </author>
    <author>
      <person>
        <first-name>D.H.</first-name>
        <last-name>Turner</last-name>
      </person>
    </author>
    <title>Expanded Sequence Dependence of Thermodynamic Parameters 
    Improves Prediction of RNA Secondary Structure</title>
    <journal>J. Mol. Biol.</journal>
    <volume>288</volume>
    <issue>5</issue>
    <pages>911,994</pages>
    <date>
      <year>1999</year>
    </date>
  </reference>
</rnaml>
