Because a protein-encoding gene is composed of nucleotides in triplets as codons, more effective Markov models are built in sets of three nucleotides, describing nonrandom distributions of trimers or hexamers, and so on.

Gene and promoter prediction is a crucial research area in bioinformatics. Accurate prediction of promoters is important for understanding gene function and regulation, and for interpreting gene expression patterns.

Topics include: Categories of Gene Prediction Programs, Gene Prediction in Prokaryotes, & Gene Prediction in Eukaryotes.