XML output format (Description)

Gene extracted from a human prediction (XML format) 
<?xml version="1.0" ?>
<!DOCTYPE prediction SYSTEM "geneid.dtd">

<prediction locus="AF100956_AF027865" length="140000" source="geneid_v1.2" 
    date="Thu Sep 27 12:52:58 2001" genes="10" score ="204.19">
...
   <gene idGene="AF100956_AF027865.G5" strand ="fwd" exons="6" score="12.35">
      <exon idExon="AF100956_AF027865.G5E1" type="First" frame="0" score="5.38">
         <site idSite="AF100956_AF027865.G5E1S1" type="Start" position="65038" score="3.06" />
         <site idSite="AF100956_AF027865.G5E1S2" type="Donor" position="65220" score="2.89" />
      </exon>
      <exon idExon="AF100956_AF027865.G5E2" type="Internal" frame="0" score="-0.93">
         <site idSite="AF100956_AF027865.G5E2S1" type="Acceptor" position="65872" score="2.58" />
         <site idSite="AF100956_AF027865.G5E2S2" type="Donor" position="66019" score="0.44" />
      </exon>
      <exon idExon="AF100956_AF027865.G5E3" type="Internal" frame="2" score="-0.44">
         <site idSite="AF100956_AF027865.G5E3S1" type="Acceptor" position="66210" score="2.20" />
         <site idSite="AF100956_AF027865.G5E3S2" type="Donor" position="66321" score="3.78" />
      </exon>
      <exon idExon="AF100956_AF027865.G5E4" type="Internal" frame="1" score="2.57">
         <site idSite="AF100956_AF027865.G5E4S1" type="Acceptor" position="66774" score="2.22" />
         <site idSite="AF100956_AF027865.G5E4S2" type="Donor" position="66903" score="3.50" />
      </exon>
      <exon idExon="AF100956_AF027865.G5E5" type="Internal" frame="0" score="4.80">
         <site idSite="AF100956_AF027865.G5E5S1" type="Acceptor" position="67344" score="2.54" />
         <site idSite="AF100956_AF027865.G5E5S2" type="Donor" position="67548" score="1.45" />
      </exon>
      <exon idExon="AF100956_AF027865.G5E6" type="Terminal" frame="2" score="0.97">
         <site idSite="AF100956_AF027865.G5E6S1" type="Acceptor" position="67811" score="4.31" />
         <site idSite="AF100956_AF027865.G5E6S2" type="Stop" position="67899" score="0.00" />
      </exon>
      <protein length="289">
        MALLDLCGAARGQRPEWAALDAGSGGRSDPGHYSFSAQAPELALPRGMQVRTVGRSGEMQ
        EPTAFLRSFGGDQERNVQIEMAHGTTTLAFKFQHGVIVAVDSRATAGSYISSLRMNKVIE
        INPYLLGTMSGCAADCQYWERLLAKECRLYYLRNGERISVSAASKLLSNMMLQYRGMGLS
        MGSMICGWDKKGPGLYYVDDNGTRLSGQMFSTGSGNTYAYGVMDSGYRQDLSPEEAYDLG
        RRAIAYATHRDNYSGGVVNMYHMKEDGWVKVESSDVSDLLYKYGEAAL*
      </protein>
   </gene>
...
</prediction>


Description of columns (gff format)
XML headers XML Version and DTD used
Prediction Prediction as a collection of genes
Gene Gene as a collection of exons
Exon Gene as a couple of sites
Site Splice site or transcription signal description
Key Predicted protein


To see more details about XML format, click here



Enrique Blanco Garcia © 2003