Bioinformatics도전과제중 하나. (= GeneFinding)
HMM이나, NeuralNetwork등의 MachineLearning방법들이 사용된다. procaryote에 대해서는 HMM으로 95%이상 해결된 문제이나, eucaryot에 대해서는 RnaSplicing등의 복잡한 메커니즘들로 인해 아직 미지수
관련 프로그램
for eucaryot : GenScan, Fgenesh, Grail, GeneFinder, SNAP
Prokaryotic ORF prediction
AbInitio (intrinsic) prediction
- ECOPARSE (Krogh et al. 1994)
GeneHacker (Yada and Hirosawa 1996)
GeneMark HMM (Lukashin and Borodovsky 1998)
Glimmer (Salzberg et al. 1998; Delcher et al. 1999)
- GeneMarkS (Besemer et al. 2001)
EasyGene (Larsen and Krogh 2003)
- ZCURVE (Guo et al. 2003)
GeneLook (Nishi et al. 2005)
Homology-base (extrinsic) prediction
Integration of AbInitio (intrinsic) and homology-based (extrinsic) predictions
Orpheus (Frishman et al., 1998)
- - DPS (Dna-Protein Search) against the Nr database
- Critica (Badger and Olsen 1999)
- - BLASTN against the related genome chosen by the user
- FrameD (Schiex et al., 2003)
- - BLASTX output provided by the user
- YACOP (Tech and Merkl 2003)
- - Integration of Critica, Glimmer and Zcurve