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Introduction to Bioinformatics
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
The Swiss Institute of Bioinformatics
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Collaborative structure Lausanne - Geneva
Groups at ISREC, Ludwig Institute, CHUV, Unil,
HUG, UniGe, and recently UniBas
Several roles: research, services, teaching
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DEA (master degree) in Bioinformatics: 1 year full time.
EMBnet courses: 2x 1 week per year, to be extended
Pregrade courses in Geneva, Fribourg and Lausanne
Universities
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Projects at SIB
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Databases
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Softwares
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Melanie, Deep View, proteomic tools, ESTScan, pftools, Java
applets
Services
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SWISS-PROT, PROSITE, EPD, World-2DPAGE, SWISS-MODEL
TrEST, TrGEN (predicted proteins), tromer (transcriptome)
Web servers ExPASy, EMBnet
Teaching and helpdesk
Research
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Mostly sequence and expression analysis, 3D structure, and
proteomic
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
EMBnet organisation
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European in 1988, now world-wide spread
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29 country nodes, 9 special nodes.
Role
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Training, education
Software development (EMBOSS, SRS)
Computing resources (databases, websites, services)
Helpdesk and technical support
Publications
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Swiss node http://www.ch.embnet.org
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Other important sites
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ExPASy - Expert Protein Analysis System
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EBI - European Bioinformatics Institute
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www.ebi.ac.uk
NCBI - National Center for Biotechnology
Information
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www.expasy.org
www.ncbi.nlm.nih.gov
Sanger - The Sanger Institute
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www.sanger.ac.uk
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Bioinformatics: definition
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Every application of computer science to biology
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Sequence analysis, images analysis, sample management,
population modelling, …
Analysis of data coming from large-scale biological
projects
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Genomes, transcriptomes, proteomes, metabolomes, etc…
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
The new biology
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Traditional biology
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Small team working on a specialized topic
Well defined experiment to answer precise questions
New « high-throughput » biology
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Large international teams using cutting edge technology
defining the project
Results are given raw to the scientific community without
any underlying hypothesis
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Example of « high-throughput »
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Complete genome sequencing
Large-scale sampling of the transcriptome (EST)
Simultaneous expression analysis of thousands of genes (DNA
microarrays, SAGE)
Large-scale sampling of the proteome
Protein-protein analysis large-scale 2-hybrid (yeast, worm)
Large-scale 3D structure production (yeast)
Metabolism modelling
Simulations
Biodiversity
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Role of bioinformatics
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Control and management of the data
Analysis of primary data e.g.
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Base calling from chromatograms
Mass spectra analysis
DNA microarrays images analysis
Statistics
Database storage and access
Results analysis in a biological context
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
First information: a sequence ?
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Nucleotide
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RNA (or cDNA)
Genomic (intron-exon)
Complete or incomplete?
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mRNA with 5’ and 3’ UTR regions
Entire chromosome
Protein
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Pre/Pro or functional protein?
Function prediction
Post-translational modifications?
Holy Grail: 3D structure?
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Genomes in numbers
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Sizes:
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virus: 103 to 105 nt
bacteria: 105 to 107 nt
yeast: 1.35 x 107 nt
mammals: 108 to 1010 nt
plants: 1010 to 1011 nt
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Gene number:
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virus: 3 to 100
bacteria: ~ 1000
yeast: ~ 7000
mammals: ~ 30’000
Plants: 30’000-50’000?
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Sequencing projects
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« small » genomes (<107): bacteria, virus
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« large » genomes (107-1010) eucaryotes
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Many already sequenced (industry excluded)
More than 90 microbial genomes already in the public domain
More to come! (one new every two weeks…)
12 finished (S.cerevisiae, S. Pombe, E. cuniculi, C.elegans,
D.melanogaster, A. gambiae, D. rerio, F. rubripes, A.thaliana, O.
sativa, M. musculus, Homo sapiens)
Many more to come: rat, pig, cow, maize (and other plants),
insects, fishes, many pathogenic parasites (Plasmodium…)
EST sequencing
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Partial mRNA sequences
~12x106 sequences in the public domain
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Human genome
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Size: 3 x 109 nt for a haploid genome
Highly repetitive sequences 25%, moderately repetitive
sequences 25-30%
Size of a gene: from 900 to >2’000’000 bases (introns
included)
Proportion of the genome coding for proteins: 5-7%
Number of chromosomes: 22 autosomal, 1 sexual chromosome
Size of a chromosome: 5 x 107 to 5 x 108 bases
centromer
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
exons of a gene
regulatory elements
locus control region
repetitive sequences
LF-2002.08
telomer
How to sequence the human genome?
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Consortium « international » approach:
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Generate genetic maps (meiotic recombination) and pseudogenetic
maps (chromosome hybrids) for indicator sequences
Generate a physical map based on large clones (BAC or PAC)
Sequence enough large clones to cover the genome
« commercial » approach (Celera):
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Generate random libraries of fixed length genomic clones (2kb and
10kb)
Sequence both ends of enough clones to obtain a 10x coverage
Use computer techniques to reconstitute the chromosomal
sequences, check with the public project physical map
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Sequencing progression
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Interpretation of the human draft
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Still many gaps and
unordered small pieces
(except for chr 6, 7, 20, 21,
22, Y)
Even a genomic sequence
does not tell you where the
genes are encoded. The
genome is far from being
« decoded »
One must combine genome
and transcriptome to have a
better idea
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
The transcriptome
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The set of all functional RNAs (tRNA, rRNA, mRNA
etc…) that can potentially be transcribed from the
genome
The documentation of the localization (cell type)
and conditions under which these RNAs are
expressed
The documentation of the biological function(s) of
each RNA species
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Public draft transcriptome
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Information about the expression specificity and the
function of mRNAs
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« full » cDNA sequences of know function
« full » cDNA sequences, but « anonymous » (e.g. KIAA or DKFZ
collections)
EST sequences
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cDNA libraries derived from many different tissues
Rapid random sequencing of the ends of all clones
ORESTES sequences
Growing set of expression data (microarrays, SAGE etc…)
Increasing evidences for multiple alternative splicing and
polyadenylation
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Example mapping of ESTs and mRNAs
mRNAs
ESTs
Computer prediction
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
The proteome
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Set of proteins present in a particular cell type
under particular conditions
Set of proteins potentially expressed from the
genome
Information about the specific expression and
function of the proteins
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Information on the proteome
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Separation of a complex mixture of proteins
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Individual characterisation of proteins
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2D PAGE (IEF + SDS PAGE)
Capillary chromatography
Tryptic peptides signature (MS)
Sequencing by chemistry or MS/MS
All post-translational modifications (PTMs) !
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Tridimentional structures
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Methods to determine structures
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Data format
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X-ray cristallography
NMR
Atoms coordinates (except H) in a cartesian space
Databases
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For proteins and nucleic acids (RSCB, was PDB)
Independent databases for sugars and small organic
molecules
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Visualisation of the structures
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Secondary structure elements
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Alpha helices, beta sheets, other
Softwares
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Various representations (atoms, bonds, secondary…)
Big choice of commercial and free software (e.g.,
DeepView)
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08
Sequence information, and so what ?
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How to store and organise ?
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How to access, search, compare ?
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Databases (next lecture)
Pairwise alignments, BLAST (tomorrow)
EST clustering, Multiple Alignments (Wednesday)
Patterns, PSI-BLAST, Profiles and HMMs (Thursday)
Gene prediction (Thursday)
Your problems?
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Friday
Swiss Institute of Bioinformatics
Institut Suisse de Bioinformatique
LF-2002.08