They identified several measures which are particularly useful. Methods differ in how the reference set is obtained and how the measure of fit is calculated. Reference sets that incorporate information about the amino acid composition of the potential gene are superior to those that do not. Hexamers have proven useful. The presence of STOP codons.
Most methods only consider ORFs.
However, it is possible to incorporate stop codons into a measure of amino acid content. Amino acid content. Measures of protein function, such as vectors of amino acids, dipeptides and hydrophobicity, can be obtained a potential exon. Like the codon usage vectors, these are compared to a reference set. This, however, may limit identification to particular types of protein-coding genes.