PMID:8367304
| Citation |
Cardon, LR, Burge, C, Schachtel, GA, Blaisdell, BE and Karlin, S (1993) Comparative DNA sequence features in two long Escherichia coli contigs. Nucleic Acids Res. 21:3875-84 |
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| 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. |
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| Keywords |
Base Sequence; Chromosomes, Bacterial; DNA, Bacterial/genetics; Escherichia coli/genetics; Molecular Sequence Data; Oligonucleotides; Repetitive Sequences, Nucleic Acid; Rho Factor/metabolism; Sequence Homology, Nucleic Acid; Terminator Regions, Genetic |
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