Bioinformatics Vol. 16 no. 11 2000
Pages 968-977
© 2000 Oxford University Press
Original Paper |
Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis
1 Laboratório
Nacional de
Computação
Científica, MCT,
Petrópolis, RJ, 25651-070, Brazil
2 Centro de Estudos em
Telecomunicações,
PUC/RJ, Rio de Janeiro, RJ, 22453-900, Brazil
3 Instituto de
Biofísica Carlos Chagas
Filho, UFRJ, Rio de Janeiro, RJ, 21941-590, Brazil
Received on March 18, 2000
; revised on June 6, 2000
; accepted on June 6, 2000
Motivation: The importance of the various kinds of repetitive nucleotide sequences 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 Neisseria meningitidis Z2491 and MC58. A tool has been developed based upon a statistical hypothesis test taking into account the markovian structure of random sequences in order to determine the non-random character of extragenic palindromes.
Results: Totals of 7631, 12904, 4722 and 5477 non-random short interrupted palindromes have been found on the E.coli, H.influenzae, and N.meningitidis serogroup A and serogroup B genomes, respectively. Their distribution patterns on the respective genomes vary according to the bacterial species considered. Based on their position on the genome, palindromes could be distinguished as those which integrate longer, repetitive sequences; those which stand in isolation, and still others are associated to specific genome sites.
Availability: The complete list of the observed palindromes is available at the site http://www/lncc.br/~atrv.
Contact: atrv{at}lncc.br
**** To whom correspondence should be addressed at Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis.