COMPARATIVE DNA-SEQUENCE FEATURES IN 2 LONG ESCHERICHIA-COLI CONTIGS

The recent sequencing of two relatively long (approximately 100 kb) co ntigs of E.coli presents unique opportunities for investigating hetero geneity and genomic organization of the E.coli chromosome. We have eva luated 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 distribution s 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) sequenc e similarities between the long contigs and other E.coli sequences; (i v) characterization and identification of rare and frequent oligonucle otides; (v) compositional biases in short oligonucleotides; and (vi) p osition-dependent fluctuations in sequence composition. The two contig s reveal a number of distinctive features, including: a cluster of fiv e repeat/dyad elements with very regular spacings resembling a transcr iption attenuator in one of the contigs; REP elements, ERICs, and othe r long repeats; distinction of the Chi sequence as the most frequent o ligonucleotide; regions of clustering, overdispersion, and regularity of certain restriction sites and short palindromes; and comparative do mains of inhomogeneities in the two long contigs. These and other feat ures are discussed in relation to the organization of the E.coli chrom osome.