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 A B C D 7 11 6 14 9
Otu et al. Bioinformatics, 2003

4. Correlation of Input Sequence with Group
NJ method
Smallest Sum of Branch Lengths A B C D
-40
-34
Saitou et al. Mol. Biol. Evol., 1987

5. NJ Method Leaf Length Distance to Node New Distance Matrix AB C D 5 8AB C D 5 8 7
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: Query Sequence Classification:
Distance Matrix Calculation: O(n2l2)
Query Sequence Classification:
Distance Calculation: O(nl2)
NJ Construction: O(n3)

8. Thank you