Results

The number of exon assemblies is huge; However, the spliced alignment algorithm is fast enough to process large genomic fragments (up to 180,000 nucleotides) containing multi-exon genes (more than 30 exons). After the highest-scoring exon assembly is found, the hope is that it represents the correct exon-intron structure. This is almost guaranteed if a protein sufficiently similar to the one encoded in the analyzed fragment is available (99% correlation between predicted and actual genes with mammalian targets). This method is good only if you have the right protein to compare it with. It can identify up to 53% of all genes.