title: Skewed oligomers and origins of replication.
abstract: The putative origin of replication in prokaryotic genomes can be located by a new method that finds short oligomers whose orientation is preferentially skewed around the origin. The skewed oligomer method is shown to work for all bacterial genomes and one of three archaeal genomes sequences to date, confirming known or predicted origins in most cases and in three cases (H. pylori, M. thermoautotrophicum, and Synechocystis sp.), suggesting origins that were previously unknown. In many cases, the presence of conserved genes and nucleotide motifs confirms the predictions. An algorithm for finding these skewed seven-base and eight-base sequences is described, along with a method for combining evidence from multiple skewed oligomers to accurately locate the replication origin. Possible explanations for the phenomenon of skewed oligomers are discussed. Explanations are presented for why some bacterial genomes contain hundreds of highly skewed oligomers, whereas others contain only a handful.
authors.affiliation: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. salzberg@tigr.org
authors.forename: S L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: A J
authors.initials: AJ
authors.lastname: Salzberg
authors.forename: A R
authors.initials: AR
authors.lastname: Kerlavage
authors.forename: J F
authors.initials: JF
authors.lastname: Tomb
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000235:genetics; D001483:Base Sequence; D015748:Borrelia burgdorferi Group / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics; D016678:Genome; D016680:Genome, Bacterial; D006193:Haemophilus influenzae / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics; D009161:Mycobacterium / Q000235:genetics; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D018741:Replication Origin; D016415:Sequence Alignment
chemical_list: D009838:Oligodeoxyribonucleotides