An Introduction To Sequence Comparison and Database Search

UAB, 2021

Cedric Notredame


This course is an 4 hours primer on sequence alignments. Its goal is to present an overview of the basic concepts of sequence alignments and some of their applications. The first two hours will be dedicated to molecular evolution. We will focus on the implications of molecular evolution on sequence variation. We will use these concepts to define homology. We will then see how specific mathematical models (the substitution matrices) have been derived in order to quantify the evolutionary relationship between sequences. The next two hours will be used to introduce the Needleman and Wunsch algorithm (Dynamic programming), a very basic algorithm that makes it possible to derive pairwise alignments from the sequences while using the substitution matrices.

Send your Questions to:

1.1UABLECTURESPairwise comparisons in an evolutionary context - Introduction Slides Voiceover
1.2UABLECTURESPairwise comparisons in an evolutionary context - 1 Slides Voiceover
1.3UABLECTURESPairwise comparisons in an evolutionary context - 2 Slides Voiceover
2.1UABLECTURESSubstitution Matrices Slides Voiceover
2.2UABLECTURESComparing Sequences Slides Voiceover
2.3UABLECTURESIntroduction to Dynamic Programming -1 Slides Voiceover
2.4UABLECTURESIntroduction to Dynamic Programming -2 Slides Voiceover
3UABPRACTICALSDynamic Programming (Perl) P
3UABPRACTICALSDynamic Programming (Python)P Voiceover


1. Claverie and Notredame, Bioinformatics for Dummies, 2007, Wiley

2. Durbin et al., Biological Sequence Analysis, 1999, Oxford Press

3. Patthy, Protein Evolution, 2007, Wiley

This website was automatically generated using BED, the Bioinformatics Exercise Database. BED is a freeware available on request Cedric Notredame