The Computer Journal, Volume 42, Issue 1, pp.110, 1999.
Compression and approximate matching
L. Allison, D. Powell and T. I. Dix
Abstract
A population of sequences is called nonrandom if there is a
statistical model and an associated compression algorithm that
allows members of the population to be compressed, on average.
Any available statistical model of a population should be
incorporated into algorithms for alignment of the sequences and
doing so changes the rank order of possible alignments in general.
The model should also be used in deciding if a resulting approximate match
between two sequences is significant or not.
It is shown how to do this for two plausible interpretations involving
pairs of sequences that might or might not be related.
Efficient alignment algorithms are described for quite
general statistical models of sequences.
The new alignment algorithms are more sensitive to
what might be termed 'features' of the sequences.
A natural significance test is shown to be rarely fooled by
apparent similarities between two sequences that are
merely typical of all or most members of the population,
even unrelated members.

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[doi:10.1093/comjnl/42.1.1]['05]
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Also see:
D. R. Powell,
L. Allison,
T. I. Dix,
ModellingAlignment for NonRandom Sequences,
17th ACS Australian Joint Conf. on
Artificial Intelligence (AI2004),
SpringerVerlag,
LNCS/LNAI 3339,
isbn:3540240594,
pp.203214, 2004,
(including software).
The method makes the charactermatching
scoring function context dependent and
allows "features" of sequences to be weighted appropriately.
