LEHIGH CSE 397 - Genome Rearrangements (65 pages)

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Genome Rearrangements



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Genome Rearrangements

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Lecture Notes


Pages:
65
School:
Lehigh University
Course:
Cse 397 - Issues in Cybersecurity

Unformatted text preview:

Genome Genome Rearrangements Rearrangements and and YOU YOU Presented by Kevin Gaittens Overview Bio background Definitions and Set up Reality Desire Good Components Bad Components Fin Biological Bakground Comparing entire genomes across species Need distance measure Interested in larger differences than just single insertions deletions etc Genome Rearrangements chromosome piece gene being moved or copied to another location or transferring to another chromosome altogether Definitions Block section of genome possibly containing more than one gene one unit Homologous when two blocks contain the same genes Homologous blocks have the same number label Reversal reversing a series of blocks and also their orientations distance is measured in number of reversals Example of Reversal 3 4 1 2 5 3 2 1 4 5 Red right orientation Black left orientation Goals Want shortest number of reversals to transform one genome to another Parsimony assumption assume Nature changes optimally Desire polynomial time solution Oriented has a poly time solution unoriented NP hard Example 1 2 3 4 5 5 2 1 3 4 Add circle if orientation changes One solution 1 2 3 4 5 1 2 5 4 3 1 2 5 3 4 5 2 1 3 4 Breakpoints Act as a minimum Happens in the case of first last label in original not the first last label in the target OR 2 labels are consecutive in original but not in target OR consecutive in original and target but duel orientation is different between blocks 5 4 and 5 4 NOTE If a pair of labels is an exact reversal in the target there is NO breakpoint 4 5 and 5 4 do not have a breakpoint Breakpoints for Last Example 1 2 3 4 Goal reminder 5 2 1 3 5 4 1 is different than first of target No breakpoint between 1 and 2 since exact reversal in target 2 and 3 not consecutive in target 3 and 4 match thus no breakpoint 4 and 5 are not consecutive in target 5 is different from last in target Mathy Stuff o Let L be finite set of labels L0 U a a for all a in L x remove arrows Ex a a a Cont d Oriented permutation



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