lab2(Hedi-Ayari): Sequence alignment implementation

[Hedi-Ayari]

Week 2 Sequence Alignment PR Checklist

General

• I have read the Contributing Guide
• I have read the Git Workflow Guide
• I understand the Code of Conduct

Demo Scripts

• I ran demo01_pairwise.py successfully (demonstrates Biopython global/local alignment)
• I ran demo02_distance_matrix.py successfully (computes sequence distances)

Exercises

• I completed ex02_global_nw.py (Needleman-Wunsch global alignment implementation)
• I completed ex03_local_sw.py (Smith-Waterman local alignment implementation)
• Both exercises use proper matrix initialization and scoring functions
• Both exercises include correct backtracking algorithms

Submissions

• I created the directory labs/02_alignment/submissions/<github_handle>/
• I added Hedi-Ayari_notes.md with datasets used and reflection on global vs local alignment
• I added the completed ex02_global_nw.py to my submissions directory
• I added the completed ex03_local_sw.py to my submissions directory

Datasets

• I used TP53 sequences from data/sample/tp53_dna_multi.fasta for testing
• I understand the difference between global and local alignment algorithms
• I can explain when to use each alignment type

Pull Request

• My PR title follows the format: lab2(<handle>): Sequence alignment implementation
• My PR description includes a summary of implemented algorithms
• I targeted the correct base repository and branch (bozdogalex/bioinf-y4-lab:main)
• I have not pushed any data files to the repository (they remain in data/work/)

Learning Outcomes

• I understand global vs local alignment differences
• I can implement basic NW and SW algorithms
• I know when to prefer global over local alignment
• I can interpret alignment results and scores