Introduction to Bioinformatics

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Introduction to Bioinformatics
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SIB and EMBnet Bioinformatics resources for
biomedical scientists
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The Swiss Institute of Bioinformatics

• Founded in March 1998
• Collaborative structure Lausanne - Geneva - Basel
• Groups at ISREC, Ludwig Institute, Unil, HUG,
  UniGe, recently UniBas and soon EPFL.
• Several roles teaching, services, research
• Currently 130 employees

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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

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Teaching

• DEA (master degree) in Bioinformatics 1 year
  full time, first diploma common to Unige and
  Unil.
• EMBnet courses 2x 1 week per year in Lausanne,
  to be extended in Basel
• Pregrade courses in Geneva, Fribourg and Lausanne
  Universities
• Other courses at CHUV and EPFL
• Courses in other countries Colombia, Cambodia,
  Peru,

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Research

• New algorithms (faster alignments)
• New technology (GRID or cluster computing)
• New tools (protein analysis, microarrays,
  confocal microscopy)
• New databases (microarrays, transcriptome,
  proteome)
• Collaborations with lab researchers!

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Three levels of services

• Simple web access to softwares and databases
• Easy to use for basic occasional research with
  few sequences
• Potentially insecure
• Command-line access with a local Unix account
• More powerful (automation) and secure
• Requires to understand Unix system and frequent
  practice
• Collaboration with SIB
• Access to experts in the field (help desk)
• For projects requiring huge programming or
  special hardware resources

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SIBs important sites

• Home
• www.isb-sib.ch
• ExPASy - Expert Protein Analysis System
• www.expasy.org
• Hits database and tools
• hits.isb-sib.ch
• EMBnet Switzerland
• www.ch.embnet.org
• Geneva Bioinformatics
• www.genebio.ch

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SIB home
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Expert Protein Analysis System
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Swiss node http//www.ch.embnet.org
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EMBnet organisation

• European in 1988, now world-wide spread
• 32 country nodes, 8 special nodes.
• Role
• Training, education (EMBER)
• Software development (EMBOSS, SRS)
• Computing resources (databases, websites,
  services)
• Helpdesk and technical support
• Publications (EMBnet.news, Briefings in
  Bioinformatics)
• Access www.embnet.org
• Each node with www.xx.embnet.org where xx is
  the country code (e.g., ch for Switzerland)

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EMBnet home
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European Molecular Biology Open Software Suite

• Free Open Source (for most Unix plateforms)
• GCG successor (compatible with GCG file format)
• More than 200 programs
• Easy to install locally
• but no interface, requires local databases
• Unix command-line only
• Interfaces
• Jemboss, www2gcg, w2h, wemboss (with account)
• Pise, EMBOSS-GUI (no account)
• Access www.emboss.org

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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

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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

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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

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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

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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

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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?

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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 30000
• Plants 30000-50000?

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Sequencing projects

•  small  genomes (lt107) bacteria, virus
• Many already sequenced (industry excluded)
• More than 100 microbial genomes already in the
  public domain
• More to come! (one new every two weeks)
•  large  genomes (107-1010) eucaryotes
• 15 finished (S.cerevisiae, S. Pombe, E. cuniculi,
  G. theta, C.elegans, D.melanogaster, A. gambiae,
  P. falciparum, P. yoelii, D. rerio, F. rubripes,
  A.thaliana, O. sativa (2x), M. musculus, Homo
  sapiens)
• Many more to come rat, pig, cow, maize (and
  other plants), insects, fishes, many pathogenic
  parasites (Leishmania)
• EST sequencing
• Partial mRNA sequences 15x106 sequences in the
  public domain

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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 gt2000000 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

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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

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Sequencing progression
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Interpretation of the human draft

• Still many gaps and unordered small pieces
  (except for chr 6, 7, 13, 14 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

Last freeze Ncbi30 June 24, 2002
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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

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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

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Example mapping of ESTs and mRNAs
mRNAs
ESTs
Computer prediction
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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

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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) !

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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

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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)

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Sequence information, and so what ?

• How to store and organise ?
• Databases (next lecture)
• How to access, search, compare ?
• Pairwise alignments, dot plots (Tuesday)
• BLAST searches in db (Tuesday)
• EST clustering (Wednesday)
• Multiple Alignments (Wednesday)
• Patterns, PSI-BLAST, Profiles and HMMs (Thursday)
• Gene prediction (Thursday)
• Protein function prediction (Friday)
• Users problems (Friday)

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Thank you