We hold that the reliance on ab initio approaches presents difficulties, as known genes may be more highly expressed and may present a biased sample for calibration. Another difference in the approaches is that we have used pre-assembled consensus transcripts whenever possible in alignment to the genome. The use of such consensus sequences is likely to improve alignment, increase splicing evidence, and has been shown to improve the detection of protein homology [19]. We propose that the remaining 32,000-42,000 units we have identified will represent a useful resource for additional investigation as genomic annotation proceeds. A comparison of all three approaches will surely yield new insights.