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Protein Sequence Classification Using Neighbor-Joining Method

Protein Sequence Classification Using Neighbor-Joining Method. Bo Liu. Overview. Given: A group of sequences, they have somewhat similarity between each other and same protein function. Input: One unknown function sequence Output: If this sequence belongs to this protein cluster. .

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Protein Sequence Classification Using Neighbor-Joining Method

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  1. Protein Sequence Classification Using Neighbor-Joining Method Bo Liu

  2. Overview • Given: A group of sequences, they have somewhat similarity between each other and same protein function. • Input: One unknown function sequence • Output: If this sequence belongs to this protein cluster.

  3. Representation of Sequences Group • Distance Matrix • Matrix Calculation • Pair-Wise Alignment • Multiple Sequence Alignment • Alignment-Free: Relative Lempel-Ziv Complexity Otu et al. Bioinformatics, 2003

  4. Correlation of Input Sequence with Group • NJ method • Smallest Sum of Branch Lengths Saitou et al. Mol. Biol. Evol., 1987

  5. NJ Method • Leaf Length • Distance to Node • New Distance Matrix Studier et al. Mol. Biol. Evol., 1988

  6. Classification Criteria • Node with longest leaf length. • Evolve too fast • Last node joined into the tree. • Cost the most to join the tree

  7. Running Time • Preprocessing: • Distance Matrix Calculation: O(n2l2) • Query Sequence Classification: • Distance Calculation: O(nl2) • NJ Construction: O(n3)

  8. Thank you

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