Local Alignment and Statistics

This course, from the MIT Open Courseware library, provides an overview of the principles and tools used in classical and next-generation sequencing. The second half of the course covers BLAST- Basic Local Alignment Search Tool- which is an algorithm that allows a researcher to compare a query sequence with a larger set of sequences. This course is the second lecture in a larger Foundations of Computational and Systems Biology course taught at MIT in Spring 2014.

Learning Objectives:

• Describe the process of conventional sequencing technologies
• Define the Sanger Sequencing method
• Identify examples and characteristics of conventional sequencing technologies
• Distinguish between various next generation sequencing technologies
• Highlight the benefits of local alignment
• Develop a BLAST-like algorithm
• Define statistics of matching
• Target frequencies and mismatch penalties for nucleotide alignments 

1. Overview - 3 minutes

   1. What do you already know?
   2. Overview and objectives

2. Conventional Sequencing - 10 minutes

   1. 1D, 2D, and 3D models of DNA
   2. Sanger Sequencing Method
   3. Practical Examples of Conventional Sequencing
   4. Read Lengths of Conventional Sequencing

3. Next Gen Sequencing - 10 minutes 

   1. Next Generation Sequencing Technologies
   2. Roche Technology
   3. Illumina Technology
   4. Helicose and Pac Bio Technologies
   5. Deeper Dive into Roche Technology
   6. Deeper Dive into Illumina Technology

4. Local Alignment - 15 minutes

   1. Why Align Sequences?
   2. Finding Top Scoring Alignment Matches
   3. Creating an Algorithm to Find Top Matches
   4. Calculating Running Time
   5. Expected Score Has to Be Negative

5. Deeper Dive into the Algorithm  - 10 minutes

   1. Identifying Frequency of High Scoring Segments Across a Sequence
   2. Calculating Lambda
   3. What Happens to Lambda If Scores Are Doubled? 
   4. What Does Lambda Mean?

6. Scoring Matrix and Mismatch Penalty - 8 minutes

   1. What Scoring Matrix to Use for DNA
   2. Choosing the Mismatch Penalty

7. Wrap Up - 2 minutes

   1. What Do You Know Now?