Pairwise Sequence Alignment

Pairwise Sequence Alignment

• Sequence comparison lies at the heart of bioinformatics analysis

• Process by which sequences are compared by searching for common

character patterns

• Nucleotide bases and amino acids are the building blocks of DNA &
proteins

• These molecules can be considered molecular fossils that encode the

history of millions of years of evolution.
 DNA/Protein

Mutations
 
 DNA/Protein

Mutations
 
 Sequence Sequence Sequence
homology similarity identity
Qualitative - Quantitative

- Percentage of aligned residues

that are similar in physiochemical
properties
At what similarity level can one infer homologous relationship?

Image taken from Essential Bioinformatics by Jin Xiong

 The goal is to find the best possible alignment between two sequences

Local alignment

Methods
Global
alignment
 What is dynamic programming?

• Breaking down a larger problem into smaller sub-problems/tasks

• Solves each sub-problem in order to solve the bigger problem

• A computational method to find the best optimal alignment between

two sequences
• The method compares every character in the two sequences and
generates an alignment
 Global vs. Local alignment

• Global
• Align both sequences end-to-end
• Good for sequences that are very similar and of same length

• Local
• Align stretches of sequence with the highest density of matches
• Generates more than one aligned region (sub-alignments)
• Good for aligning sequences that are similar at only some positions and differ at
others
• Good for sequences that vary in length or that share a conserved domain or
motif
Next topics that we will discuss:

1. Dot plot method of aligning two sequences

2. Global Alignment
3. Local alignment