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Home ยป Sequence Alignment

Sequence Alignment

Sequence Similarity Introduction

This lesson and exercise defines similarity in a non-biological and biological sense, quantifies the similarity between two sequences, explains how a substitution matrix is used to quantify similarity, calculates amino acid similarity scores using the BLOSUM 62 substitution matrix, explains how BLAST detects similarity between two sequences and how to use BLAST and interpret the alignments.
PowerPoint
PowerPoint
Handout
Handout
Tables
Tables
Sequences
Sequences

Introduction to R and RStudio

This series of modules introduces students to the statistical platform R using an integrated development environment of RStudio. Both softwares can be downloaded for free. Once downloaded and installed according to Module 0, students should watch the accompanying video for an introduction to the new environment. Module 1 presents an exercise where students work with genomic sequence alignment data to learn how to construct R commands while performing basic summary statistics and making basic plots.

From Smith-Waterman to BLAST

This lecture from Dr. Jeremy Buhler discusses the limitations of the Smith-Waterman local alignment algorithm and the heuristics used by the BLAST program in order to reduce the search space and to quickly produce high-scoring local alignments.