geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.

In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons.

Geneid is used at Ouest Genopole.