Lecture 1: Introduction to Bioinformatics

Improved from Burr Settles

bsettles@cs.wisc.edu
www.cs.wisc.edu/~bsettles/i
bs08/
and Kerstin Wagner

Copyright© Kerstin Wagner

What is bioinformatics?
 “Bioinformatics”
• Before the era of bioinformatics, only two ways of performing
biological experiments were available:
• Within a living organism (so-called in vivo) or in an artificial
environment (so-called in vitro, from the Latin in glass)
• Taking the analogy further, we can say that bioinformatics is in fact in
silico biology, from the silicon chips on which microprocessors are
built
• More specifically, we can define bioinformatics as the computational
branch of molecular biology
 “Bioinformatics”
• Bioinformatics created from the interaction of biology and computer
science
• Uses computer databases and computer algorithms (a series of steps
followed to solve logical and mathematical problems by computer) to
analyze proteins, genes, and the complete collections of
deoxyribonucleic acid (DNA) that comprises an organism (the
genome).
• Used for solving biological problems
– data problems: representation (graphics), storage and retrieval
(databases), analysis (e.g. statistics)
– biology problems: sequence analysis, structure or function
prediction, data mining, etc.
 Database
storage

You are
here

Copyright© Kerstin Wagner

 The Commercial Market
• Current bioinformatics market is worth 300 million / year
• Prediction: increase by $2 billion / year in 5-6 years
• ~50 Bioinformatics companies:

Genomatrix Software, Genaissance Pharmaceuticals, Lynx, Lexicon Genetics,

DeCode, Genetics, CuraGen, AlphaGene, Bionavigation, Pangene, InforMax,
TimeLogic, GeneCodes, LabOnWeb.com, Darwin, Celera, Incyte, BioResearch
Online, BioTools, Oxford Molecular, Genomica, NetGenics, Rosetta, Lion
BioScience, DoubleTwist, eBioinformatics, Prospect Genomics, Neomorphic,
Molecular Mining, GeneLogic, GeneFormatics, Molecular Simulations,
Bioinformatics Solutions….

Copyright© Kerstin Wagner

But how did bioinformatics arise?
Huge amount of molecular information
was being generated

Drew Sheneman, New Jersey--The Newark Star Ledger

 Pre-Computer Era:

• Molecular sequences were assembled, analysed, and compared by:

• Manually writing them on pieces of paper,
• Taping them side by side on laboratory walls,
• And/or moving them around for optimal alignment (now called
pattern matching)
• You can imagine how labour intensive this maybe
 Solution
• Set up of computers and algorithms
that allow:
• Access, processing, storing, sharing,
retrieving, visualizing,…..
• Bioinformatics coined in 1960s
• Margaret Oakley Dayhoff created: IBM 7090 computer

• The first protein database

• The first program for sequence
assembly
 Significance of Bioinformatics
• Molecular medicine
– identification of genetic components for various conditions that
help in diagnosis based on sequence or gene expression
– determine appropriate gene therapy
• Pharmacogenomics
– developing highly targeted drugs
• Toxicogenomics
– elucidating which genes are affected by various chemicals
Focus of Bioinformatics
 Approaches to Bioinformatics
• The first perspective or approach on bioinformatics is the cell:
Molecular Biology main focus is on individual genes, messenger
RNA (mRNA) transcripts, and proteins
• But:
The focus of bioinformatics is the complete collection of DNA (the
genome),RNA (the transcriptome),and protein sequences(the
proteome) that have been collected
• genome = complete set of genes present in a cell or organism),
transcriptome= all set of messenger RNA expressed in a single cell or set
of cells),proteome = all set of proteins that is or can be expressed in a
cell, tissue or organism)
• Bioinformatics can help answer biological questions that can be
approached from levels ranging from:
• Cellular phenotype is all the distinct components of multiple
cellular processes involving gene and protein expression that result
in the elaboration of a cell's particular morphology and function.
 Approaches to Bioinformatics
• Second perspective focuses on individual organisms:
• Here bioinformatics tools can be applied to describe changes through
developmental time, changes across body regions, and changes in a
variety of physiological or pathological states
• For example - Gene expression varies in disease states or in response
to a variety of signals, both internal and environmental
• Expressed genes and proteins derived from different tissues and
conditions.
• DNA microarrays measure the expression of thousands of genes in
biological samples
Second approach to Bioinformatics
 Approaches to Bioinformatics
• Third perspective focuses on multiple species (tree of
life):
• Here the focus is on the variations that occur
between species and among members of a species
where we can deduce the evolutionary history of life
on Earth.
• Uses comparative genomics in which genomes are
compared
Third approach to Bioinformatics
Databases
 Molecular Databases
• Publicly available databanks now contain billions of nucleotides of DNA
sequence data collected from thousands of different organisms.
• > 300 other publicly available databases pertaining to molecular biology
• GenBank
> 61 million sequence entries > 65 billion bases
• UnitProtKB / Swis-Prot
> 277 thousand protein sequence entries > 100 million amino acids
• Protein Data Bank
45,632 protein (and related) structures
• * all numbers current about 9/07
 Thursday: Chapter 2
•Access to sequence data and
literature information
• Read before class