Nucleic Acids Research, Vol 26, Issue 12 2971-2980, Copyright © 1998 by Oxford University Press
EPC Rocha, A Viari and A Danchin
We present a general analysis of oligonucleotide usage in the complete
genome of Bacillus subtilis . Several datasets were built in order to
assign various biological contexts to the biased use of words and to reveal
local asymmetries in word usage that may be coupled with replication, the
control of gene expression and the restriction/modification system. This
analysis was complemented by cross-comparisons with the complete genomes of
Escherichia coli , Haemophilus influenzae and Methanococcus jannaschii . We
have observed a large number of biased oligonucleotides for words of size
up to 8, throughout the datasets and species, indicating that such long
strict words play an important role as biological signals. We speculate
that some of them are involved in interactions with DNA and/or RNA
polymerases. An extensive analysis of palindrome abundances and
distributions provides the surprising result that prophage-like elements
embedded in the genome exhibit a smaller avoidance of restriction sites.
This may reinforce a recently proposed hypothesis of a selfish gene
phenomena in the transfer of restriction/modification systems in bacteria.
ARTICLES
Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons
Atelier de BioInformatique, Universite Paris VI, 12 Rue Cuvier, 75005 Paris, France. crocha@abi.snv.jussieu.fr
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