“Integrated” gene models: GHMMs
Genie
- Generalized hidden Markov model with length distribution
- Integration of multiple content and signal sensors
- Content: codon statistics, repeats, intron, intergenic, database homology hits
- Signal: promoter, start codon, splice sites, stop codon
- Dynamic programming to find optimal parse
- Several genes per sequence possible
- Kulp et al. (1996), ISMB, 4, 134-142.
- Reese et al. (1997), JCB, 4(3), 311-323.
- http://www.cse.ucsc.edu/~dkulp/cgi-bin/genie