We present an independent comparative analysis of seven recently developed 
gene-finding programs: FGENES, GeneMark.hmm, Genie, Genescan, HMMgene, Morgan, 
and MZEF. For evaluation purposes we developed a new, thoroughly filtered, and 
biologically validated dataset of mammalian genomic sequences that does not 
overlap with the training sets of the programs analyzed. Our analysis shows that 
the new generation of programs has substantially better results than the 
programs analyzed in previous studies. The accuracy of the programs was also 
examined as a function of various sequence and prediction features, such as G + 
C content of the sequence, length and type of exons, signal type, and score of 
the exon prediction. This approach pinpoints the strengths and weaknesses of 
each individual program as well as those of computational gene-finding in 
general. The dataset used in this analysis (HMR195) as well as the tables with 
the complete results are available at http://www.cs.ubc.ca/~rogic/evaluation/.