edit_distance

edit_distance - University of North Texas Biocomputing...

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    Biocomputing University of North Texas Dynamic Programming: Edit Distance Source: www.bioalgorithms.info
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  University of North Texas Biocomputing DNA Sequence Comparison: First Success Story Finding sequence similarities with genes of known function is a common approach to infer a newly sequenced gene’s function In 1984 Russell Doolittle and colleagues found similarities between cancer-causing gene and normal growth factor (PDGF) gene
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  University of North Texas Biocomputing Cystic Fibrosis Cystic fibrosis (CF) is a chronic and frequently fatal genetic disease of the body's mucus glands (abnormally high level of mucus in glands). CF primarily affects the respiratory systems in children. Mucus is a slimy material that coats many epithelial surfaces and is secreted into fluids such as saliva
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  University of North Texas Biocomputing Cystic Fibrosis: Mutation Analysis If a high % of cystic fibrosis (CF) patients have a certain mutation in the gene and the normal patients don’t, then that could be an indicator of a mutation that is related to CF A certain mutation was found in 70% of CF patients, convincing evidence that it is a predominant genetic diagnostics marker for CF
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  University of North Texas Biocomputing Cystic Fibrosis and CFTR Gene : CFTR (Cystic Fibrosis Transmembrane conductance Regulator)
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  University of North Texas Biocomputing Mechanism of Cystic Fibrosis The CFTR protein (1480 amino acids) regulates a chloride ion channel Adjusts the “wateriness” of fluids secreted by the cell Those with cystic fibrosis are missing one single amino acid in their CFTR Mucus ends up being too thick, affecting many organs
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  University of North Texas Biocomputing Bring in the Bioinformaticians Gene similarities between two genes with known and unknown function alert biologists to some possibilities Computing a similarity score between two genes tells how likely it is that they have similar functions Dynamic programming is a technique for revealing similarities between genes The Change Problem is a good problem to introduce the idea of dynamic programming
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  University of North Texas Biocomputing The Change Problem Goal : Convert some amount of money M into given denominations, using the fewest possible number of coins Input : An amount of money M , and an array of d denominations c = ( c 1 , c 2 , , c d ), in a decreasing order of value ( c 1 > c 2 > … > c d ) Output : A list of d integers i 1 , i 2 , , i d such that c 1 i 1  + c 2 i 2  + … + c d i d  =  M and i 1 + i 2 + … + i d is minimal
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  University of North Texas Biocomputing Change Problem: Example Given the denominations 1, 3, and 5, what is the minimum number of coins needed to make change for a given value?
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edit_distance - University of North Texas Biocomputing...

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