For transcriptome analysis, it is critical to precisely define all the transcripts across the whole genome. More and more digital gene expression (DGE) scannings have indicated the presence of huge amount of novel transcripts in addition to the known gene models. However, almost all these studies still depend crucially on existing annotation. Here, we present Gene2DGE, a Perl software package for gene model renewal with DGE data. We applied Gene2DGE to the mouse blastomere transcriptome, and defined 98,532 read-enriched regions (RERs) by read clustering supported by more than four reads for each base pair. Taking advantage of this ab initio method, we refined 2,104 exonic regions (4% of a total of 48,501 annotated transcribed regions) with remarkable extension into un-annotated regions (>50 bp). For 5% of uniquely mapped reads falling within intron regions, we identified 13,291 additional possible exons. As a result, we renewed 4,788 gene models, which account for 39% of a total of 12,277 transcribed genes. Furthermore, we identified 12,613 intergenic RERs, suggesting the possible presence of novel genes outside the existing gene models. In this study, therefore, we have developed a suitable tool for re-newal of known gene models by ab initio prediction in transcriptome dissection. The Gene2DGE package is freely available at http://bighapmap.big.ac.cn/.
