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Bioinformatics for Biotechnology students

Introduction to Alignments

1. Introduction to Sequence Alignments
2. Representations of pairwise alignments

Algorithms for Pairwise Alignments

3. Needleman-Wunsch Algorithm: Global Alignment
4. Code: Global pairwise alignments
5. Smith-Waterman Algorithm: Local Alignment
6. Code: Local Pairwise alignment
7. Semi-global Alignment
8. Code: Semi-global pairwise alignment

Protein Sequence Alignment

9. Aligning Proteins
10. Code: Aligning amino acid sequences

Multiple Sequence Alignments

11. Multiple Sequence Alignments
12. Code for Progressive multiple sequence alignments
13. Profile Hidden Markov Models
14. Code describing the Viterbi algorithm

Sequence Retrieval

15. The BLAST Algorithm for Sequence Retrieval
16. Code for BLAST-styled queries

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By Lukas Käll

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