Week 2 — Extended Module

Day 1: Working with a Single Protein Sequence (5 hours)

• Lecture (2 hours):
• Predicting physico-chemical properties (molecular weight, pI) using ProtParam.
• Primary structure analysis: Hydrophobicity plots and transmembrane segment prediction.
• Introduction to protein domains and post-translational modifications.
• Practical (3 hours):
• Using ProtParam to analyze a protein sequence.
• Generating and interpreting a hydrophobicity plot with ProtScale.
• Introduction to domain databases (Pfam, InterPro).
• Practical challenge: From a given DNA sequence, find the longest ORF, translate it, and analyze the resulting protein's properties.

Day 2: The Power of Similarity Searching

• Sequence Similarity Searching (5 hours)
• Lecture (2 hours):

• The concept of homology and its importance.
• Introduction to BLAST: Different flavors (blastp, blastn, blastx, etc.).
• Understanding BLAST output: E-value, bit score, and alignments.

• Practical (3 hours):

• Running a blastp search on the NCBI server.
• Interpreting the graphical output, hit list, and individual alignments.

Day 3: Advanced Similarity Searching (5 hours)

• Lecture (2 hours):

• Controlling BLAST parameters: Substitution matrices, gap penalties, and filters.
• Introduction to PSI-BLAST for finding distant relatives.
• Practical and tasks (3 hours):
• Running a PSI-BLAST search and iterating to find more homologs.
• Using BLAST to find protein domains.
• BLAST Clinic: Bring your sequence and interpret the results with the instructor's help.
• Case study: Using BLAST to infer the function of an unknown protein.