GeneExpression-UniversityofCalifornia,SantaBarbara基因表达-加利福尼亚大学，圣塔巴巴拉.pptVIP

Genome RearrangementSORTING BY REVERSALS Comparative Genomics Problem Definition During biological evolution, inter- and intra-chromosomal? exchanges of chromosomal fragments disrupt the order of genes on a? chromosome. The genome rearrangements approach, is the use of? combinatorial optimization techniques, to infer a sequence of rearrangement events to account for the differences among the? genomes.? Outline Genome Comparison In the late 1980 was discovered remarkable and novel pattern of evolutionary change in plant organelles. Jeffrey Palmer and his collegues compared the mitochondrial genomes of cabbage and turnip, which are very closely related. Molecules which are almost identical in gene sequences, differ dramatically in gene order. {Sridhar, Pevzner 1995} This discovery and many other studies proved that genome rearrangements represent a common mode of molecular evolution. Cabbage and Turnip Single Chromosome Operations Operations on 2 Chromosomes Genomic Sorting Problem Given genomes the genomic sorting problem is to find a series of reversals where and t is minimal. We call t the genomic distance between Outline What is a Permutation? Permutation (?) : an ordered arrangement of the set { 1,2,…,n} Signed Permutation (?): a permutation where the elements are oriented a reversal switches element orientation {+3 -4 +7 -6 +1 -5 +2 } ?(7,-5) = {+3 -4 +5 -1 +6 -7 +2} Let i ~ j if | i – j | = 1. Extend permutation by adding = 0 and = n + 1. We call pair of elements , 0 ≤ i ≤ n, of an adjacency if ~ and a breakpoint if is not ( ~ ) Breakpoint graph – signed case Correlation between the breakpoints and reversal dista