Predicted gene structures using different grades of genomic sequence. The annotated relative positions of exons in the rat CAPZA2 (A), baboon CAV2 (B), and lemur GASZ (C) genes are indicated. In each case, the exon positions predicted by Genscan (Burge and Karlin 1997) using each of the different types of genomic sequence are shown below (generated for BAC clones RP31-188L2 [GenBank no. AC087041], RP41-479B1 [GenBank no. AC084730], and LB2-246N5 [GenBank no. AC123544], respectively). The positions of gaps in the full-shotgun draft and comparative-grade finished sequence are shown as grey boxes. Note that using full-shotgun draft sequence (with unordered contigs separated by stretches of 50 Ns), Genscan incorrectly predicts the positions of a number of exons whose positions are correctly predicted by using comparative-grade finished sequence (with ordered and oriented contigs separated by stretches of 50 Ns) or human-grade finished sequence. There are also cases in which Genscan incorrectly predicts exons using all three types of sequence.
