Begin at the beginning: predicting genes with 5' UTRs.

The retrainable, comparative gene predictor N-SCAN integrates multigenome modeling and 5' untranslated region (5' UTR) modeling. In this article, we evaluate N-SCAN's transcription-start site (TSS) and first exon predictions both computationally and experimentally. The computational results indicate that N-SCAN is more accurate than any of the other tools we tested at predicting the TSS and the complete first exon. It is the only one of these tools that can predict complete gene structures together with 5' UTRs. Experimental evaluation shows that N-SCAN can be used to validate novel UTR introns in human gene predictions that do not overlap any RefSeq gene and even to correct RefSeq mRNAs by adding validated UTR exons that are missing from RefSeq.