title: Comparative DNA sequence features in two long Escherichia coli contigs.
abstract: The recent sequencing of two relatively long (approximately 100 kb) contigs of E.coli presents unique opportunities for investigating heterogeneity and genomic organization of the E.coli chromosome. We have evaluated a number of common and contrasting sequence features in the two new contigs with comparisons to all available E.coli sequences (> 1.6 Mb). Our analyses include assessments of: (i) counts and distributions of restriction sites, special oligonucleotides (e.g., Chi sites, Dam and Dcm methylase targets), and other marker arrays; (ii) significant distant and close direct and inverted repeat sequences; (iii) sequence similarities between the long contigs and other E.coli sequences; (iv) characterization and identification of rare and frequent oligonucleotides; (v) compositional biases in short oligonucleotides; and (vi) position-dependent fluctuations in sequence composition. The two contigs reveal a number of distinctive features, including: a cluster of five repeat/dyad elements with very regular spacings resembling a transcription attenuator in one of the contigs; REP elements, ERICs, and other long repeats; distinction of the Chi sequence as the most frequent oligonucleotide; regions of clustering, overdispersion, and regularity of certain restriction sites and short palindromes; and comparative domains of inhomogeneities in the two long contigs. These and other features are discussed in relation to the organization of the E.coli chromosome.
authors.affiliation: Department of Mathematics, Stanford University, CA 94035.
authors.forename: L R
authors.initials: LR
authors.lastname: Cardon
authors.forename: C
authors.initials: C
authors.lastname: Burge
authors.forename: G A
authors.initials: GA
authors.lastname: Schachtel
authors.forename: B E
authors.initials: BE
authors.lastname: Blaisdell
authors.forename: S
authors.initials: S
authors.lastname: Karlin
mesh_terms: D001483:Base Sequence; D002876:Chromosomes, Bacterial; D004269:DNA, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D008969:Molecular Sequence Data; D009841:Oligonucleotides; D012091:Repetitive Sequences, Nucleic Acid; D012234:Rho Factor / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D013728:Terminator Regions, Genetic
chemical_list: D004269:DNA, Bacterial; D009841:Oligonucleotides; D012234:Rho Factor