RIblast extension-stop heuristics

Fulanko / IntaRNA

Efficient target prediction incorporating accessibility of interaction sites

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RIblast extension-stop heuristics #3

Closed martin-raden closed 5 years ago

martin-raden commented 5 years ago

RIblast stopt interaction prediction, wenn es nicht besser wird = heuristik

check https://github.com/fukunagatsu/RIblast wie genau implementiert
schreibs entsprechend formal auf
implementier die strategie als neuen predictor

martin-raden commented 5 years ago

new PredictorMfe2dSeedExtensionRiBlast implementieren
aufschrieb anpassen
prelim benchmark

martin-raden commented 5 years ago

./src/bin/IntaRNA -q guuucccc -t gggggcaaac --seedbp=4 --energy=B --tacc=N --qacc=N

martin-raden commented 5 years ago

add example to docu

./src/bin/IntaRNA -t CCCAUUUCC -q GGGGG --seedTQ="8||&1||" --seedbp=2 --model=X
# vs
./src/bin/IntaRNA -t CCCAUUUCC -q GGGGG --seedTQ="8||&1||" --seedbp=2 --model=X --mode=R

martin-raden commented 5 years ago

disadvantage: overweighting parallel seed extension advantage: no explicit max-interaction length needed