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Genome Res. 15:742-747, 2005
©2005 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/05 $5.00
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Begin at the beginning: Predicting genes with 5' UTRs

Randall H. Brown2, Samuel S. Gross1,2 and Michael R. Brent3

Laboratory for Computational Genomics, Washington University, St. Louis, Missouri 63130, USA

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.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3696205.

2 These authors have contributed equally to this work.

1 Present address: Computer Science Department, Stanford University, Stanford, CA 94305.

3 Corresponding author.
E-mail brent{at}cse.wustl.edu; fax (314) 935-7302.


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