greedy - University of North Texas Biocomputing 1...

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Unformatted text preview: University of North Texas Biocomputing 1 Biocomputing University of North Texas Greedy Algorithms And Genome Rearrangements University of North Texas Biocomputing Turnip vs Cabbage: Look and Taste Different • Although cabbages and turnips share a recent common ancestor, they look and taste different University of North Texas Biocomputing Turnip vs Cabbage: Comparing Gene Sequences Yields No Evolutionary Information University of North Texas Biocomputing 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 University of North Texas Biocomputing Turnip vs Cabbage: Different mtDNA Gene Order • Gene order comparison: Before After Evolution is manifested as the divergence in gene order University of North Texas Biocomputing Transforming Cabbage into Turnip University of North Texas Biocomputing 2 University of North Texas Biocomputing • 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 University of North Texas Biocomputing History of Chromosome X Rat Consortium, Nature , 2004 University of North Texas Biocomputing Reversals • Blocks represent conserved genes. 1 3 2 4 10 5 6 8 9 7 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 University of North Texas Biocomputing Reversals 1 3 2 4 10 5 6 8 9 7 1, 2, 3, -8, -7, -6, -5, -4, 9, 10 ¡ Blocks represent conserved genes. ¡ In the course of evolution or in a clinical context, blocks 1,…,10 could be misread as 1, 2, 3, -8, -7, -6, -5, -4, 9, 10. University of North Texas Biocomputing Reversals: Example 5’ ATG CCTGTA CTA 3’ 3’ TAC GGACAT GAT 5’ 5’ ATG TACAGG CTA 3’ 3’ TAC ATGTCC GAT 5’ Break and Invert University of North Texas Biocomputing Types of Rearrangements Reversal 1 2 3 4 5 6 1 2-5 -4 -3 6 Translocation 1 2 3 4 5¡¡ 6 1 2 6 4 5 3 1 2 3 4 5 6 1 2 3 4 5 6 Fusion Fission University of North Texas Biocomputing 3 University of North Texas Biocomputing Comparative Genomic Architectures: Mouse vs Human Genome • Humans and mice have similar genomes, but their genes are ordered differently • ~245 rearrangements • Reversals • Fusions • Fissions • Translocation University of North Texas Biocomputing Waardenburg ’ s Syndrome: Mouse Provides Insight into Human Genetic Disorder • Waardenburg’s syndrome is characterized by pigmentary dysphasia • Gene implicated in the disease was linked to human chromosome 2 but it was not clear where exactly it is located on chromosome 2 University of North Texas Biocomputing Waardenburg ’ s syndrome and splotch mice...
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This note was uploaded on 04/15/2011 for the course BIOL 1130 taught by Professor Roberts during the Spring '08 term at North Texas.

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greedy - University of North Texas Biocomputing 1...

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