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Distance Calculation Correction Using Regression

Distance Calculation Correction Using Regression. An Improvement in Phylogenetic Tree Reconstruction from Gene Order Data. Walker Pett Divya Mistry. Our Problem. Current algorithms assume that genome rearrangements would go through minimum number of possible steps

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Distance Calculation Correction Using Regression

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  1. Distance Calculation Correction Using Regression An Improvement in Phylogenetic Tree Reconstruction from Gene Order Data Walker Pett DivyaMistry

  2. Our Problem • Current algorithms assume that genome rearrangements would go through minimum number of possible steps • This is not how nature works • Popular algorithms assume that given gene order data must have gone through only one type of rearrangement • Usually not true in nature. For a sequence of rearrangements, one may have been inversion and another transposition.

  3. Our Solution • Step A: Allow more than one type of rearrangement events to occur at a pre-determined probability • Instead of allowing transpositions or inversions exclusively, provide both events some probabilities of occurring, and simulate the tree production • Output A: Tree with possible rearrangements • Step B: Overcome the issue of algorithm assuming minimum number of steps • Use non-linear regression to find corrected distance from the optimal distance produced by the algorithm • Output B: Apply the knowledge gained from regression analysis to perform better tree reconstruction

  4. Step A demystified • For a given series of rearrangements in gene order data, we may assume • Only one type of rearrangement occurs • classical approach • All the different types of rearrangements have equal chances • better than classical approach • Allow the biologists to decide which rearrangements are legal and with what probability • Better than previous two, but relies on Biologist to have prior knowledge about origins of the data

  5. Step A demystified • (Possible to put a picture of output of a tree from our program?) • Even an ASCII version of tree would be alright, because we can explain what is going on. Let me know what you think.

  6. Step B demystified • We just put a picture with actual data, expected data, and point out our suggested correction. • Since we just have to show how we are using stuff we learned in class, a sample image where we just point out what we are doing to solve the problem… should suffice. Yea?

  7. References • Moret BM et.al.New Approaches for Reconstructing Phylogenies from Gene Order Data. Bioinformatics. 2001. 17 Suppl 1:S165-73 • Anything else you want to cite?

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