Transforming men into mice (polynomial algorithm for genomicdistance problem)
Hannenhalli, S.; Pevzner, P.A.
Foundations of Computer Science, 1995. Proceedings., 36th Annual Symposium on
Volume , Issue , 23-25 Oct 1995 Page(s):581 - 592
Digital Object Identifier 10.1109/SFCS.1995.492588
Summary:Many people believe that transformations of humans into mice
happen only in fairy tales. However, despite some differences in
appearance and habits, men and mice are genetically very similar. In the
pioneering paper, J.H. Nadeau and B.A. Taylor (1984) estimated that
surprisingly few genomic rearrangements (178±39) happened since
the divergence of human and mouse 80 million years ago. However, their
analysis is nonconstructive and no rearrangement scenario for
human-mouse evolution has been suggested yet. The problem is complicated
by the fact that rearrangements in multi chromosomal genomes include
inversions, translocations, fusions and fissions of chromosomes, a
rather complex set of operations. As a result, at first glance, a
polynomial algorithm for the genomic distance problem with all these
operations looks almost as improbable as the transformation of a (real)
man into a (real) mouse. We prove a duality theorem which expresses the
genomic distance in terms of easily computable parameters reflecting
different combinatorial properties of sets of strings. This theorem
leads to a polynomial time algorithm for computing most parsimonious
rearrangement scenarios. Based on this result and the latest comparative
physical mapping data we have constructed a scenario of human-mouse
evolution with 131 reversals/translocaitons/fusions/fissions. A
combination of the genome rearrangement algorithm with the recently
proposed experimental technique called ZOO FISH suggests a new
constructive approach to the 100 year old problem of reconstructing
mammalian evolution
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