Very Fast Identification of RNA Motifs in Genomic DNA. Application to tRNA Search in the Yeast Genome

Abstract

A common strategy characterises the various methods independently 1 Institut Gaspard Monge defined to identify almost unambiguously different types of RNA Université de Marne-la-Vallée, 2 rue de la molecules in DNA fragments. So far, the good quality of detection of RNA motif has been the prior motivation and effectively delayed the Butte Verte, 93166 optimisation of programs. As an illustration of possible improvements, a Noisy-le-Grand Cedex, France modified version of tRNAscan is described. The previous algorithm was 2 Laboratoire Informatique et altered to run 500 times faster and to lower both rates of false positives Génome, Université de and false negatives. The newly sequenced genome of Saccharomyces Versailles-Saint-Quentin cerevisiae is scanned both ways in less than three minutes and results match 45 avenue des Etats-Unis annotations found in databanks with three exceptions, two of which being 78035 Versailles Cedex arguably not real tRNAs. France