Programming for Bioinformatics

Module 2 - Sequence Alignment

Learning Outcomes

At the end of instruction, students will be able to:

• Tell what is an algorithm
• Write Python functions implementing algorithms
• Describe how to compare protein structures
• Describe how to compare protein sequences
• Explain what is a substitution matrix
• Describe the differences between PAM and BLOSUM matrices
• Use a substitution matrix to determine the similarity of two sequences
• Write a Python function implementing an exhaustive pairwise alignment algorithm
• Discuss dynamic programming strategies
• Implement dynamic programming algorithms in Python
• Calculate the statistical significance of a pairwise alignment
• Discuss similarity searches in databases
• Describe main differences between FASTA and BLAST

Mid term exam

Date: Tuesday, 13 Jan 2019 Consisting in:

• One exercise or an open ended question to assess the ability to discuss substitution matrices
• A script assessing the ability to implement a basic pairwise alignment algorithm in Python