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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