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