Chum::Result::MotifPrediction::MotifPredictionXMLReader - Reads standardized XML results from motif prediction algorithms output. This internally standardizes results.
Example: <output> <predicted_motif score="27.51" seq="TTAACTAA"> <matrix name="All occurrences" type="PFM"> <index A="213" C="13" G="10" T="16" position="8"/> <index A="186" C="38" G="16" T="12" position="7"/> <index A="33" C="42" G="4" T="173" position="6"/> <index A="32" C="152" G="17" T="51" position="5"/> <index A="218" C="7" G="6" T="21" position="4"/> <index A="213" C="14" G="4" T="21" position="3"/> <index A="13" C="17" G="11" T="211" position="2"/> <index A="15" C="17" G="6" T="214" position="1"/> </matrix> <hit name="-1sequences16" score="95.73" sequence="TTAATTAA" start="135" strand="-1"/> <hit name="-1sequences16" score="89.35" sequence="TTAGTGAA" start="330" strand="-1"/> </predicted_motif> <predicted_motif> ...
Stephen Montgomery (smontgom@bcsgc.bc.ca)