Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis

Motivation: The importance of the various kinds of repetitive nucleotide se quences for the workings of bacterial DNA has been widely recognized. This work is concerned with the distribution of a particular group of repetitive sequences, the short-sequenced interrupted extragenic palindromes, on the genetic maps of Escherichia coli K-12, Haemophilus influenzae Rd and Neisse ria meningitidis Z2491 and MC58. A tool has been developed based upon a sta tistical hypothesis test taking into account the markovian structure of ran dom sequences in order to determine the non-random character of extragenic palindromes. Results: Totals of 7631, 12 904, 4722 and 5477 non-random short interrupted palindromes have been found on the E.coli, H.influenzae, and N.meningitidi s serogroup A and serogroup B genomes, respectively. Their distribution pat terns on the respective genomes vary according to the bacterial species con sidered. Based on their position on the genome, palindromes could be distin guished as those which integrate longer repetitive sequences; those which s tand in isolation, and still others are associated to specific genome sites .