[[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, [[Orpheus]] 
 * for eucaryot : GenScan, [[Fgenesh]], [[Grail]], GeneFinder, [[SNAP]]

== Prokaryotic ORF prediction ==

'''AbInitio (intrinsic) prediction'''
  
  1. GeneMark (Borodovsky and McIninch 1993)
  1. ECOPARSE (Krogh et al. 1994)
  1. GeneHacker (Yada and Hirosawa 1996)
  1. GeneMark HMM (Lukashin and Borodovsky 1998)
  1. [[Glimmer]] (Salzberg et al. 1998; Delcher et al. 1999)
  1. GeneMarkS (Besemer et al. 2001)
  1. EasyGene (Larsen and Krogh 2003)
  1. ZCURVE (Guo et al. 2003)
  1. 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
 1. Critica (Badger and Olsen 1999)
   - BLASTN against the related genome chosen by the user
 1. FrameD (Schiex et al., 2003)
   - BLASTX output provided by the user
 1. YACOP (Tech and Merkl 2003)
   - Integration of Critica, Glimmer and Zcurve