“Integrated” gene models: HMMs

• HMMGene

  • Several genes per sequence possible
  • User constraints possible
  • Krogh (1997), ISMB, 5, 179-186.
  • http://www.cbs.dtu.dk/services/HMMgene/

• GeneMark.hmm

  • Based on GeneMark program for bacterial sequences
  • Can predict frame shifts
  • Trained for various organisms
  • Lukashin and Borodovsky (1998), NAR, 26, 1107-1115.
  • http://genemark.biology.gatech.edu/GeneMark/hmmchoice.html

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