Table 1.

Summary of the selected tools for ab initio gene prediction in eukaryotes.

Tools	Years	Main sequence features	Algorithms
GeneID	1992 [50]	Splice sites; Start and stop codons; Coding signals	Rule-based system
GeneParser	1993 [51]	Splice site; Codon usage; Compositional complexity; Hexamer frequency; Length distribution; Periodic asymmetry	Dynamic programming
GENSCAN	1997 [52]	Coding signals; Length distributions and compositional features of exons, introns and intergenic regions	Generalized hidden Markov mode
HMMgene	1997 [53]	Coding, noncoding, and intergenic sequences	Hidden Markov model
Fgenesh	2000 [54]	Splice sites; Start and stop codons; Poly (A) signals; ORFs	Hidden Markov model
AUGUSTUS	2005 [55]	Sequences around splice sites, start and stop codons, and coding and non-coding regions; Length of exons, introns and intergenic regions	Generalized hidden Markov mode

Note: only these actively cited tools are included without subjective preference.