Ch05_Rearrangements

Ch05_Rearrangements - www.bioalgorithms.info An...

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Unformatted text preview: www.bioalgorithms.info An Introduction to Bioinformatics Algorithms Greedy Algorithms And Genome Rearrangements An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Outline • Transforming Cabbage into Turnip • Genome Rearrangements • Sorting By Reversals • Pancake Flipping Problem • Greedy Algorithm for Sorting by Reversals • Approximation Algorithms • Breakpoints: a Different Face of Greed • Breakpoint Graphs An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Outline CHANGE • Genome Rearrangements – give picture of splotch mouse An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Look and Taste Different • Although cabbages and turnips share a recent common ancestor, they look and taste different An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Comparing Gene Sequences Yields No Evolutionary Information An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Almost Identical mtDNA gene sequences • In 1980s Jeffrey Palmer studied evolution of plant organelles by comparing mitochondrial genomes of the cabbage and turnip • 99% similarity between genes • These surprisingly identical gene sequences differed in gene order • This study helped pave the way to analyzing genome rearrangements in molecular evolution An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Different mtDNA Gene Order • Gene order comparison: An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Different mtDNA Gene Order • Gene order comparison: An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Different mtDNA Gene Order • Gene order comparison: An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Different mtDNA Gene Order • Gene order comparison: An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Turnip vs Cabbage: Different mtDNA Gene Order • Gene order comparison: Before After Evolution is manifested as the divergence in gene order An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Transforming Cabbage into Turnip An Introduction to Bioinformatics Algorithms www.bioalgorithms.info • What are the similarity blocks and how to find them? • What is the architecture of the ancestral genome? • What is the evolutionary scenario for transforming one genome into the other? Unknown ancestor ~ 75 million years ago Mouse (X chrom.) Human (X chrom.) Genome rearrangements An Introduction to Bioinformatics Algorithms www.bioalgorithms.info History of Chromosome X Rat Consortium, Nature , 2004 An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Reversals • Blocks represent conserved genes....
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This note was uploaded on 02/10/2012 for the course CSE 5615 taught by Professor Mitra during the Fall '11 term at FIT.

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Ch05_Rearrangements - www.bioalgorithms.info An...

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