Table 1.

The types of constraints that can be imposed by the user on the predicted gene structure

Constraint type	Meaning
Start	The translation initiation site (requires an atg in the sequence)
Stop	The translation end point (requires a stop codon)
Ass	Acceptor (3′) splice site (requires ag consensus)
Dss	Donor (5′) splice site (requires gt consensus)
Exonpart	An interval or a single position that is coding i.e. it is contained in an exon
Exon	An interval that is a complete exon
Intronpart	An interval or a single position that is contained in an intron

The constraints can refer to either strand. Exon and exonpart constraints may optionally specify a reading frame.