Lee2008

CREATED: 200705180606 LINK: url:~/Modules/Literature/Lee2008.pdf ** Motivation

• recombination
• affects accuracy of phylogenetic relationship
• recombination of biological significance

** Challenges

• strength of recombination (amount of mutation)
• timeline
• mutation rates

** Approaches

• Global reference tree
• Sliding window approach ** compare sequence on left and right side of window to detect significant difference ** base on phylogeny: PDM, Pruned PDM, RECOMP ** base on computing distance: PhyPro, DSS

** Weakness of distance based approaches

• uses hamming distance/edit distance which is not informative, does not take into account distribution of the mutations
• sensitive to choice of window length

** Contributions

• concept of shared (k,m) mers as an informatice distance measure
• positive specific weights, heavier wights near bp, lower weights away from bp
• scoring function considers chains of shared (k,m) mers

** Experiments

• three simulated datasets from Pruned PDM paper
• HepB dataset, compare with bp in literature
• finding CRF of HIV-1