Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Introduction to Bioinformatics

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

The Swiss Institute of Bioinformatics

Collaborative structure Lausanne - Geneva Groups at ISREC, Ludwig Institute, CHUV, Unil,

HUG, UniGe, and recently UniBas Several roles: research, services, teaching

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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Projects at SIB

Databases SWISS-PROT, PROSITE, EPD, World-2DPAGE, SWISS-MODEL TrEST, TrGEN (predicted proteins), tromer (transcriptome)

Softwares Melanie, Deep View, proteomic tools, ESTScan, pftools, Java

applets Services

Web servers ExPASy, EMBnet Teaching and helpdesk

Research Mostly sequence and expression analysis, 3D structure, and

proteomic

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

EMBnet organisation

European in 1988, now world-wide spread 31 country nodes, 8 special nodes. Colombia since

last September!! Role

Training, education Software development (EMBOSS, SRS) Computing resources (databases, websites, services) Helpdesk and technical support Publications

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Swiss node http://www.ch.embnet.org

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Other important sites

ExPASy - Expert Protein Analysis System www.expasy.org

EBI - European Bioinformatics Institute www.ebi.ac.uk

NCBI - National Center for Biotechnology Information www.ncbi.nlm.nih.gov

Sanger - The Sanger Institute www.sanger.ac.uk

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Bioinformatics: definition

Every application of computer science to biology Sequence analysis, images analysis, sample

management, population modelling, … Analysis of data coming from large-scale

biological projects Genomes, transcriptomes, proteomes, metabolomes,

etc…

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

The new biology

Traditional biology Small team working on a specialized topic Well defined experiment to answer precise questions

New « high-throughput » biology 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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Example of « high-throughput »

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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Role of bioinformatics

Control and management of the data Analysis of primary data e.g.

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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

First information: a sequence ?

Nucleotide RNA (or cDNA) Genomic (intron-exon) Complete or incomplete?

mRNA with 5’ and 3’ UTR regions Entire chromosome

Protein Pre/Pro or functional protein? Function prediction Post-translational modifications? Holy Grail: 3D structure?

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Genomes in numbers

Sizes: 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

Gene number: virus: 3 to 100 bacteria: ~ 1000 yeast: ~ 7000 mammals: ~ 30’000 Plants: 30’000-

50’000?

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Sequencing projects

« small » genomes (<107): bacteria, virus Many already sequenced (industry excluded) More than 90 microbial genomes already in the public

domain More to come! (one new every two weeks…)

« large » genomes (107-1010) eucaryotes 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 Partial mRNA sequences ~12x106 sequences in the public domain

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Human genome

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 exons of a gene telomer

regulatory elements repetitive sequences

locus control region

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

How to sequence the human genome?

Consortium « international » approach: 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): 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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Sequencing progression

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Interpretation of the human draft

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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

The transcriptome

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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Public draft transcriptome

Information about the expression specificity and the function of mRNAs « full » cDNA sequences of know function « full » cDNA sequences, but « anonymous » (e.g. KIAA or

DKFZ collections) EST sequences

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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Example mapping of ESTs and mRNAs

ESTsmRNAs

Computer prediction

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

The proteome

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 BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Information on the proteome

Separation of a complex mixture of proteins 2D PAGE (IEF + SDS PAGE) Capillary chromatography

Individual characterisation of proteins Tryptic peptides signature (MS) Sequencing by chemistry or MS/MS

All post-translational modifications (PTMs) !

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Tridimentional structures

Methods to determine structures X-ray cristallography NMR

Data format Atoms coordinates (except H) in a cartesian space

Databases For proteins and nucleic acids (RSCB, was PDB) Independent databases for sugars and small organic

molecules

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Visualisation of the structures

Secondary structure elements Alpha helices, beta sheets, other

Softwares Various representations (atoms, bonds, secondary…) Big choice of commercial and free software (e.g.,

DeepView)

Swiss Institute of BioinformaticsInstitut Suisse de Bioinformatique

LF-2002.10

Sequence information, and so what ?

How to store and organise ? Databases (next lecture)

How to access, search, compare ? Pairwise alignments, BLAST (tomorrow) EST clustering, Multiple Alignments (Thursday) Patterns, PSI-BLAST, Profiles and HMMs (Friday) Gene prediction (Friday) Function prediction, tools and EMBOSS (Saturday)

Your problems? Saturday