APAT: Documentation

Examples

Summary of the key aspects of the APATML DTD for per-residue annotations

<result program='NetPhos' version='2.0'>
   <function>Protein Phosphorylation sites Prediction</function>
   <run>
      ...Lists any parameters supplied to the program...
      <date>Fri Nov 19 15:30:38 GMT 2004</date>
   </run>
   <predictions>
      <perres-number name = 'P-score' clrmin = '0.0' clrmax = '1.0' 
                    graph='1' graphtype='bars'>
         <value-perres residue='1'>0.215567</value-perres>
         ...
      </perres-number>
      <threshold>
         ...<description> describes threshold...
         ...<thr-res> tags list the positive prediction residues
      </threshold> 
   </predictions>
</result> 

Summary of the key aspects of the APATML DTD for per-domain annotations

<result program='InterProScan' version='1.0'>
   <function>Protein domain Prediction</function>
   <run>
      ...Lists any parameters supplied to the program...
      <date>Fri Nov 19 15:50:04 GMT 2004</date>
   </run>
   <predictions>
      <perdom class='PRINTS' name = 'SH2_DOMAIN' highlight='1' 
              rangemin='23' rangemax='150'>
         <value-perdom label='e-value'>1.7e-17</value-perdom>
      </perdom>
      <perdom class='PROSITE' name = 'ASN_GLYCOSYLATION' highlight='0' 
              rangemin='48' rangemax='51'>
         <value-perdom label='match'>NLTV</value-perdom>
      </perdom>
      <perdom-description class='PROSITE' name = 'ASN_GLYCOSYLATION'>
         Potential N-linked glycosylation site identified by ProSite pattern.
      </perdom-description>
   </predictions>
</result> 

Summary of the key aspects of the APATML DTD for per-sequence annotations

<result program='TargetP' version='1.01'>
   <function>Protein subcellular location Prediction</function>
   <run>
      ...Lists any parameters supplied to the program...
      <date>Fri Nov 19 15:47:04 GMT 2004</date>
   </run>
   <predictions>
      <perseq name = 'mTP-pred'>
         <description>Mitochondrial targeting peptide (mTP) prediction 
                      score</description>
         <value-perseq highlight='0'>0.031</value-perseq>
      </perseq>
      <perseq name = 'Loc-pred'>
         <description>SUBCELLULAR LOCATION PREDICTION</description>
         <value-perseq highlight='1'>SECRETORY PATHWAY, i.e. THE SEQUENCE 
                                     CONTAINS A SIGNAL PEPTIDE,SP.
         </value-perseq>
      </perseq>
      ...
   </predictions>
</result>