The list of species whose complete DNA sequence have been read is growing steadily, and it
is believed that comparative genomics is in its early days. Permutations patterns (groups of
genes in some "close" proximity) on gene sequences of genomes across species is being studied
under different models, to cope with this explosion of data. The challenge is to (intelligently
and efficiently) analyze the genomes in the context of other genomes. In this paper, we present a
generalized model that uses three notions, gapped permutation patterns (with gap g), genome
clusters, via quorum, K>1, parameter, and, possible multiplicity in the patterns. The task
is to automatically discover all permutation patterns (with possible multiplicity), that occur
with gap g in at least K of the given m genomes. We present
(log mN
I + |Σ|log|Σ|N
O)
time algorithm where m is the number of sequences, each defined on Σ, N
I is the size of
the input and N
O is the size of the maximal gene clusters that appear in at least K of the m
genomes.
