SST versus EST in Gene Recognition (Invited Paper)

The EST data provide a powerful tool for identi cation of transcribed DNA sequences. However, since ESTs are relatively short, many exons are poorly covered by ESTs thus reducing the utility of EST data. Recently, SST (Signature Sequence Tags) ngerprints were proposed as an alternative to EST ngerprints. Given a ngerprint set of probes, SST of a clone is a subset of probes from the ngerprint set that hybridize with the clone. We demonstrate that besides being a powerful technique for screening cDNA libraries, SST technology provides for a very accurate gene predictions. Even with a small ngerprint set (600-800 probes) SST-based gene recognition outperforms many conventional and EST-based methods. The increase in the size of ngerprint set to 1500 probes provides almost perfect gene recognition. Even more importantly, SST-based gene predictions miss very few exons and therefore provide an opportunity to bypass cDNA sequencing step on the way from nished genomic sequence to mutation detection in gene hunting projects. Since SST data can be obtained in a highly parallel and inexpensive way, SST technology has a potential of substituting EST technology for gene hunting.