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Prediction of Saccharomyces cerevisiae replication origins

Prediction of Saccharomyces cerevisiae replication origins Adam M Breier*, Sourav Chatterji† and Nicholas R Cozzarelli‡ Addresses: *Graduate Group in Biophysics, University of California-Berkeley, Berkeley, CA 94720-3204, USA. †Department of Computer Science, University of California-Berkeley, Berkeley, CA 94720-3204, USA. ‡Department of Molecular and Cellular Biology, Barker Hall, University of California-Berkeley, Berkeley, CA 94720-3204, USA. Correspondence: Nicholas R Cozzarelli. E-mail: ncozzare@socrates.berkeley.edu reviews Published: 4 March 2004 Genome Biology 2004, 5:R22 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/4/R22 Received: 1 December 2003 Revised: 2 February 2004 Accepted: 4 February 2004 © 2004 Breier et al.; licensee BioMed Central Ltd | Research Open Access Prediction of Saccharomyces cerevisiae replication origins Adam M Breier Sourav Chatterjf and Nicholas R Cozzarelli Addresses Graduate Group in Biophysics University of California-Berkeley Berkeley CA 94720-3204 USA. ỶDepartment of Computer Science University of California-Berkeley Berkeley CA 94720-3204 USA. Department of Molecular and Cellular Biology Barker Hall University of California-Berkeley Berkeley CA 94720-3204 USA. Correspondence Nicholas RCozzarelli. E-mail ncozzare@socrates.berkeley.edu Published 4 March 2004 Genome Biology 2004 5 R22 The electronic version of this article is the complete one and can be found online at http genomebiology.com 2004 5M R22 Received 1 December 2003 Revised 2 February 2004 Accepted 4 February 2004 2004 Breier et al. licensee BioMed Central Ltd. This is an Open Access article verbatim copying and redistribution of this article are permitted in all media for any purpose provided this notice is preserved along with the article s original URL. Abstract Background Autonomously replicating sequences ARSs function as replication origins in Saccharomyces cerevisiae. ARSs contain the 17 bp ARS consensus sequence ACS which binds the origin recognition complex. The yeast genome contains more than 10 000 ACS matches but there are only a few hundred origins and little flanking sequence similarity has been found. Thus identification of origins by sequence alone has not been possible. Results We developed an algorithm Oriscan to predict yeast origins using similarity to 26 characterized origins. Oriscan used 268 bp of sequence including the T-rich ACS and a 3 A-rich region. The predictions identified the exact location of the ACS. A total of 84 of the top 100 Oriscan predictions and 56 of the top 350 matched known ARSs or replication protein binding sites. The true accuracy was even higher because we tested 25 discrepancies and 15 were in fact ARSs. Thus 94 of the top 100 predictions and an estimated 70 of the top 350