Table 1.

Features of CDS Prediction Programs

	rsCDS	NCBI CDS	ProCrest	DECODER	Longest-ORF	Truncated-ORF
Base method (ab initio/sequence similarity)	Homology	Both	Ab initio	Both	Ab initio	Ab initio
Detection of frameshift	Yes (any)	Yes (one)	Yes (one)	Yes (any)	No	No
Detection of stop codons in frame	Yes	No	No	No	No	No
Prediction of partial CDS	Yes	Yes	Yes	Yes	No	Yes
Detection of immature	Yes	No	No	No	No	No
Usage of sequence quality (phred score)	No	No	Yes	Yes	No	No

Features of six programs used for FANTOM2, estimated. See Methods for details