Study Guide for Exam 1

General comments

• This will be a closed-book, closed-notes, 50-minute exam with 5 or 6 questions
• The exam will cover all topics seen in class and lab up to and including Friday, September 16.
• Some questions will involve computation; therefore, bring your calculators.
• All required formulas or tables (except the dynamic programming equations) will be provided in the exam.
• Some questions will require short essay-like answers that show your understanding of key concepts covered in the course.
• Graduate students will have one question from the assigned readings

List of topics

Note. Unless stated otherwise, all topics are covered in the text

Alignments of Pairs of Sequences (Chapter 3 of text)

• Global vs. local alignments
• Scoring
• Dynamic programming: Filling the table and trace-back. Extensions to end-gap free and local alignments (former is not in text)
• Effect of gap penalties on alignments, affine gap penalty functions
• Scoring matrices
• Odd and log-odds scoring
• Substitution vs. scoring matrices
• PAM and BLOSUM matrix construction
• DNA PAM matrices
• Relative entropy

Statistics of Sequence Alignments (Chapter 4)

• Assessing alignment significance
• E vs. P values and how to use them to compare scores
• Importance of scale parameter (lambda)
• Effect of gaps
• Bayesian evolutionary distance
• Determining expected evolutionary distance based on an alignment
• Effect of choosing different substitution matrices

Multiple Sequence Alignment (Chapter 5)

• Multiple sequence alignment via dynamic programming
• SP scoring
• Star alignments (not in text)
• Profiles: computation and scoring, alignment of sequences to profiles and profiles to profiles