SST versus EST in gene recognition

The EST data provide a powerful tool for identification 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) fingerprints were proposed as an alternative to EST fingerprints. Given a fingerprint set of probes, SST of a clone is a subset of probes from the fingerprint set that hybridize with the clone. We demonstrate that besides being a powerful technique for screening cDNA libraries, SST technology provides for very accurate gene predictions. Even with a small fingerprint set (600-800 probes) SST-based gene recognition outperforms many conventional and EST-based methods. The increase in the size of fingerprint 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 finished 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