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Modification of program enables prediction of gene transcription

A modification to an "ace" gene prediction program by computer scientists at Washington University in St. Louis now enables scientists to predict the very beginnings of gene transcription start sites and where the first splice occurs thereby defining the first exon of the gene.

The modification to the gene prediction software TWINSCAN is called N-SCAN. Michael Brent, Ph.D. professor of computer science at Washington University in St. Louis, together with Samuel S. Gross, then an undergraduate at Washington University, and Randall H. Brown, Ph.D., a research scientist, report their results in the May 2005 issue of Genome Research. N-SCAN has proven to be the best program available at finding both the transcription start site (TSS) and the complete first exon in both the human and fruit fly genomes.

The addition of N-SCAN to TWINSCAN now provides genomics researchers the wherewithal to find and predict both the protein sequences produced by genes and their untranslated regions. Researchers in recent years have grown increasingly enthusiastic about the significance of untranslated regions. By understanding the functions of these regions, scientists expect to understand more about gene regulation ?how genes get turned on and off, the ignition system of our DNA, if you will.

To make the proteins that are the basic micro-machines of life, a region of the genome is copied, or "transcribed," to form a molecule called messenger RNA (mRNA). Some segments of the mRNA are then discarded, and the retained segments are spliced together. Geneticists have traditionally assumed that transcription starts within a few hundred bases of the protein-coding region. However, for nearly 40 percent of known human genes, transcription starts long before the beginning of the protein- coding region. Most of this extra-long untranslated region is then discarded by splicing the 5' untranslated region (UTR). All present gene finding systems ?except for N-SCAN ?either ignore
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Source:Washington University in St. Louis


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