Bioinformatics for Biotechnology students

This book is written with KTH’s course CB2442, Bioinformatics in mind. Some of the material has been generated with ChatGPT 4.1.

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

This work by Lukas Käll is licensed under CC BY 4.0