🧬 Sequence Alignment & Needleman-Wunsch
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# 🧬 Sequence Alignment & Needleman-Wunsch ## 1. 🎯 Learning Objectives - Explain sequence alignment as a search problem - Trace Needleman-Wunsch DP algorithm - Apply A* to sequence alignment ## 2.
🧬 Sequence Alignment & Needleman-Wunsch
1. 🎯 Learning Objectives
- Explain sequence alignment as a search problem
- Trace Needleman-Wunsch DP algorithm
- Apply A* to sequence alignment
2. 📖 Core Content
3.1 Problem Definition
Given two sequences, find optimal alignment (matches, mismatches, gaps). Example: ATCGAT and ATGAT → AT-CGAT and AT-G-AT (or AT-CGAT and ATG-AT).
3.2 Needleman-Wunsch Algorithm
DP matrix where D[i][j] = max(D[i-1][j-1]+match, D[i-1][j]+gap, D[i][j-1]+gap).
3.3 A* for Alignment
State = (i,j) position in DP matrix. Heuristic = maximum possible remaining score. Goal = (n,m).
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