ATYPICAL REGIONS IN LARGE GENOMIC DNA-SEQUENCES

Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. We describe a method using logarithms of pro babilities based on seventh-order Markov chains to rapidly identify ge nomic sequences that do not resemble models of genome organization bui lt from compilations of octanucleotide usage. Data bases have been con structed from Escherichia coli and Saccharomyces cerevisiae DNA sequen ces of >1000 nt and human sequences of >10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and prima te DNA sequences. We consider criteria for statistical significance of the results, offer possible explanations for the observed variation i n genome organization, and give additional applications of these metho ds in DNA sequence analysis.