Bioinformatics and Gene Sequence Analysis

 

PABIO/ MEBI/ PHG 536

University of Washington

 

Spring 2009

 

Weekly Notes and Resources

  1. Introduction -
    1. Introduction: Biological Sequence Information – Lecture Notes Week 1 – Monday
    2. NCBI Resources – Lecture Notes Week 1 – Wednesday
    3. Week 1 Monday – Computer exercise
    4. Week 1 Wednesday – Computer exercise
    5. Week 1 – Computer exercise with answers
    6. Biological Information Resource (BIR) for UW students
  2. DNA Sequence Analysis
    1. DNA Sequence Analysis – Lecture Notes Week 2 – Monday
    2. Computer exercise -Sample Problem
    3. Week 2 – Computer exercise
    4. Week 2 – Computer exercise with answers
    5. Class Sequences
  3. Protein Sequence Analysis
    1. Protein Sequence Analysis – Lecture Notes Week 3 – Monday
    2. Blossum 62 Amino Acid Substitution Matrix
    3. Week 3 – Computer exercise
    4. Week 3 – Computer exercise with answers
    5. Transmembrane Protein Processing
  4. Nucleotide BLAST Analysis
    1. BLAST – Lecture Notes Week 4 – Monday
    2. Week 4 – Computer exercise
    3. Week 4 – Computer exercise, answers and discussion
  5. Protein Motifs and BLAST
    1. Protein BLAST – Lecture Notes Week 5 – Monday
    2. Protein Motif – Lecture Notes Week 5 – Wednesday
    3. Week 5 – Computer exercise
    4. Week 5 – Computer exercise answers and discussion
  6. EST and Gene Structure Analysis
    1. EST – Lecture Notes Week 6 - Monday
    2. Week 6 – EST Computer exercise  
    3. Week 6 – EST Computer exercise answers and discussion
  7. SNP Analysis
    1. SNP – Lecture Notes Week 7 - Monday
    2. Week 7 - SNP Computer exercise (part 1)
    3. Week 7 – SNP Computer exercise answers and discussion
  8. Multiple Sequence Comparisons
    1. Multiple Sequence Alignment  – Lecture Notes Week 8 – Monday
    2. Week 8 – Multiple Sequence Alignment exercise
  9. Phylogenetic Analysis
    1. Phylogenetic Analysis  – Lecture Notes Week 8 – Wednesday
    2. Phylogenetic Analysis - Demo
    3. Week 9 – Phylogenetic analysis exercise
    4. Week 8,9 – Multiple sequence alignment and phylogenetics exercise answers and discussion
    5. Week 8,9 – additional exercise answers and discussion
    6. Phylip Help
  10. Protein Structure Analysis
    1. Protein Structure Analysis  – Lecture Notes Week 10 – Monday
    2. Week 10 – Protein Structure exercise

 

Takehome Final Sequence Link

Takehome Final answers

Takehome Final answers in ppt