Bioinformatics 1
Learning Objectives
• What is bioinformatics?
• Sequence identity/annotation principles
o How to understand it? What it does? Structure?
• Identification of sequence features
• Understand how ProtScale plots amino acid hydrophobicity to identify transmembrane
domains
• Understand global and local sequence alignments
• Knowledge of main sequence databases
What is bioinformatics?
• Not just a theoretical research field – has practical applications for bench scientists
• Provides valuable tools that are becoming more essential in biological research
o Used in every department
• Next generation sequencing
o Sequence projects (vast amounts of sequences/genomes identified)
o Gene expression analysis
• Identifying and understanding features in proteins
o Domains (i.e. transmembrane)
o Signal peptides
o Secondary/tertiary structures etc.
Sequence annotation
• A.a. sequence → peptide sequence → 3-D structure
• Sequence annotation: main principle is to compare unknown to known, look for similarities
o Analysis will look for sequence identity (perfect match) or sequence homology
(partial match)
o Both just as informative
o If domain is identified – this may provide important information on function
• These methods and principles of sequence homology – common to bioinformatics &
sequence annotation
• Pattern recognition → gene/sequence prediction + function
Similar concept: DNA fingerprinting
• Example of homology search
• Cut DNA genome with restriction enzyme (at specific points)
o Genome contains repeated sequences = microsatellites: small arrays of tandem
repeats e.g. dinucleotide, usually simple in sequence (1-4bp) and <100bp in length
o Different no. of repeats
• Homology/similarity can be used to demonstrate family relationships
o “Family” = concept to group proteins
PFAM Alignment
• Protein family (database) alignment
Learning Objectives
• What is bioinformatics?
• Sequence identity/annotation principles
o How to understand it? What it does? Structure?
• Identification of sequence features
• Understand how ProtScale plots amino acid hydrophobicity to identify transmembrane
domains
• Understand global and local sequence alignments
• Knowledge of main sequence databases
What is bioinformatics?
• Not just a theoretical research field – has practical applications for bench scientists
• Provides valuable tools that are becoming more essential in biological research
o Used in every department
• Next generation sequencing
o Sequence projects (vast amounts of sequences/genomes identified)
o Gene expression analysis
• Identifying and understanding features in proteins
o Domains (i.e. transmembrane)
o Signal peptides
o Secondary/tertiary structures etc.
Sequence annotation
• A.a. sequence → peptide sequence → 3-D structure
• Sequence annotation: main principle is to compare unknown to known, look for similarities
o Analysis will look for sequence identity (perfect match) or sequence homology
(partial match)
o Both just as informative
o If domain is identified – this may provide important information on function
• These methods and principles of sequence homology – common to bioinformatics &
sequence annotation
• Pattern recognition → gene/sequence prediction + function
Similar concept: DNA fingerprinting
• Example of homology search
• Cut DNA genome with restriction enzyme (at specific points)
o Genome contains repeated sequences = microsatellites: small arrays of tandem
repeats e.g. dinucleotide, usually simple in sequence (1-4bp) and <100bp in length
o Different no. of repeats
• Homology/similarity can be used to demonstrate family relationships
o “Family” = concept to group proteins
PFAM Alignment
• Protein family (database) alignment
