[Bioinformatics]도전과제중 하나. (= GeneFinding)

[HMM]이나, NeuralNetwork등의 MachineLearning방법들이 사용된다. procaryote에 대해서는 [HMM]으로 95%이상 해결된 문제이나, eucaryot에 대해서는 RnaSplicing등의 복잡한 메커니즘들로 인해 아직 미지수

관련 프로그램

• for procaryote : [Glimmer], GeneMark

• for eucaryot : GenScan, [Fgenesh], [Grail], GeneFinder

Prokaryotic ORF prediction

AbInitio (intrinsic) prediction

1. GeneMark (Borodovsky and McIninch 1993)

2. ECOPARSE (Krogh et al. 1994)

3. GeneHacker (Yada and Hirosawa 1996)

4. GeneMark HMM (Lukashin and Borodovsky 1998)

5. [Glimmer] (Salzberg et al. 1998; Delcher et al. 1999)
6. GeneMarkS (Besemer et al. 2001)

7. EasyGene (Larsen and Krogh 2003)

8. ZCURVE (Guo et al. 2003)

9. GeneLook (Nishi et al. 2005)

Homology-base (extrinsic) prediction

• Homology search algorithm : [BLAST]
• Reference database

  • SwissProt

  • UniProt

  • RefSeq protein

  • Nr

Integration of AbInitio (intrinsic) and homology-based (extrinsic) predictions

1. ORPHEUS (Frishman et al., 1998)
   • - DPS (Dna-Protein Search) against the Nr database
2. Critica (Badger and Olsen 1999)
   • - BLASTN against the related genome chosen by the user
3. FrameD (Schiex et al., 2003)
   • - BLASTX output provided by the user
4. YACOP (Tech and Merkl 2003)
   • - Integration of Critica, Glimmer and Zcurve