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    • www. .uni-rostock.de Bioinformatics Introduction to genomics and proteomics I Ulf Schmitz ulf.schmitz@informatik.uni-rostock.deBioinformatics and Systems Biology Group www.sbi.informatik.uni-rostock.de Ulf Schmitz, Introduction to genomics and proteomics I 1
    • www. .uni-rostock.deOutlineGenomics/Genetics 1. The tree of life • Prokaryotic Genomes – Bacteria – Archaea • Eukaryotic Genomes – Homo sapiens 2. Genes • Expression Data Ulf Schmitz, Introduction to genomics and proteomics I 2
    • www. .uni-rostock.deGenomics - Definitions Genetics: is the science of genes, heredity, and the variation of organisms. Humans began applying knowledge of genetics in prehistory with the domestication and breeding of plants and animals. In modern research, genetics provides tools in the investigation of the function of a particular gene, e.g. analysis of genetic interactions. Genomics: attempts the study of large-scale genetic patterns across the genome for a given species. It deals with the systematic use of genome information to provide answers in biology, medicine, and industry. Genomics has the potential of offering new therapeutic methods for the treatment of some diseases, as well as new diagnostic methods. Major tools and methods related to genomics are bioinformatics, genetic analysis, measurement of gene expression, and determination of gene function. Ulf Schmitz, Introduction to genomics and proteomics I 3
    • Genes www. .uni-rostock.de • a gene coding for a protein corresponds to a sequence of nucleotides along one or more regions of a molecule of DNA • in species with double stranded DNA (dsDNA), genes may appear on either strand • bacterial genes are continuous regions of DNA bacterium: • a string of 3N nucleotides encodes a string of N amino acids • or a string of N nucleotides encodes a structural RNA molecule of N residueseukaryote: • a gene may appear split into separated segments in the DNA • an exon is a stretch of DNA retained in mRNA that the ribosomes translate into protein Ulf Schmitz, Introduction to genomics and proteomics I 4
    • www. .uni-rostock.deGenomics Genome size comparison Species Chrom. Genes Base pairs Human 46 28-35,000 3.1 billion (Homo sapiens) (23 pairs) Mouse 40 22.5-30,000 2.7 billion (Mus musculus) Puffer fish 44 31,000 365 million (Fugu rubripes) Malaria mosquito 6 14,000 289 million (Anopheles gambiae) Fruit Fly 8 14,000 137 million (Drosophila melanogaster) Roundworm 12 19,000 97 million (C. elegans) Bacterium 1 5,000 4.1 million (E. coli) Ulf Schmitz, Introduction to genomics and proteomics I 5
    • www. .uni-rostock.deGenes exon: A section of DNA which carries the coding A section of DNA which carries the coding sequence for a protein or part of it. Exons sequence for a protein or part of it. Exons are separated by intervening, non-coding are separated by intervening, non-coding sequences (called introns). In eukaryotes sequences (called introns). In eukaryotes most genes consist of a number of exons. most genes consist of a number of exons.intron: An intervening section of DNA which occurs An intervening section of DNA which occurs almost exclusively within a eukaryotic gene, but almost exclusively within a eukaryotic gene, but which is not translated to amino-acid sequences in which is not translated to amino-acid sequences in the gene product. the gene product. The introns are removed from the pre-mature The introns are removed from the pre-mature mRNA through a process called splicing, which mRNA through a process called splicing, which leaves the exons untouched, to form an active leaves the exons untouched, to form an active mRNA. mRNA. Ulf Schmitz, Introduction to genomics and proteomics I 6
    • www. .uni-rostock.deGenes Examples of the exon:intron mosaic of genes exon intron Globin gene – 1525 bp: 622 in exons, 893 in introns Ovalbumin gene - ~ 7500 bp: 8 short exons comprising 1859 bp Conalbumin gene - ~ 10,000 bp: 17 short exons comprising ~ 2,200 bp Ulf Schmitz, Introduction to genomics and proteomics I 7
    • www. .uni-rostock.dePicking out genes in genomes • Computer programs for genome analysis identify ORFs (open reading frames) • An ORF begins with an initiation codon ATG (AUG) • An ORF is a potential protein-coding region • There are two approaches to identify protein coding regions… Ulf Schmitz, Introduction to genomics and proteomics I 8
    • www. .uni-rostock.dePicking out genes in genomes1. Detection of regions similar to known coding regions from other organisms• Regions may encode amino acid sequences similar to known proteins• Or may be similar to ESTs (correspond to genes known to be expressed)• Few hundred initial bases of cDNA are sequenced to identify a gene2. Ab initio methods, seek to identify genes from the properties of the DNA sequence itself • Bacterial genes are easy to identify, because they are contiguous • They have no introns and the space between genes is small • Identification of exons in higher organisms is a problem, assembling them another… Ulf Schmitz, Introduction to genomics and proteomics I 9
    • www. .uni-rostock.dePicking out genes in genomesAb initio gene identification in eukaryotic genomes • The initial (5´) exon starts with a transcription start point, preceded by a core promoter site such as the TATA box (~30bp upstream) – Free of stop codons – End immediately before a GT splice-signalbinds and directs RNA polymeraseto the correct transcriptional start site Ulf Schmitz, Introduction to genomics and proteomics I 10
    • www. .uni-rostock.dePicking out genes in genomes5 splice signal3 splice signal Ulf Schmitz, Introduction to genomics and proteomics I 11
    • www. .uni-rostock.dePicking out genes in genomesAb initio gene identification in eukaryotic genomes• Internal exons are free of stop codons too – Begin after an AG splice signal – End before a GT splice signal Ulf Schmitz, Introduction to genomics and proteomics I 12
    • www. .uni-rostock.dePicking out genes in genomes Ab initio gene identification in eukaryotic genomes• The final (3´) exon starts after a an AG splice signal – Ends with a stop codon (TAA,TAG,TGA) – Followed by a polyadenylation signal sequence Ulf Schmitz, Introduction to genomics and proteomics I 13
    • www. .uni-rostock.deHumans havespliced genes… Ulf Schmitz, Introduction to genomics and proteomics I 14
    • www. .uni-rostock.deDNA makes RNA makes Protein Ulf Schmitz, Introduction to genomics and proteomics I 15
    • www. .uni-rostock.deTree of life Prokaryotes Ulf Schmitz, Introduction to genomics and proteomics I 16
    • Genomics – Prokaryotes www. .uni-rostock.de• the genome of a prokaryote comes as a single double-stranded DNA molecule in ring-form – in average 2mm long – whereas the cells diameter is only 0.001mm – < 5 Mb• prokaryotic cells can have plasmids as well (see next slide)• protein coding regions have no introns• little non-coding DNA compared to eukaryotes – in E.coli only 11% Ulf Schmitz, Introduction to genomics and proteomics I 17
    • www. .uni-rostock.deGenomics - Plasmids• Plasmids are circular double stranded DNA molecules that are separate from the chromosomal DNA.• They usually occur in bacteria, sometimes in eukaryotic organisms• Their size varies from 1 to 250 kilo base pairs (kbp). There are from one copy, for large plasmids, to hundreds of copies of the same plasmid present in a single cell. Ulf Schmitz, Introduction to genomics and proteomics I 18
    • www. .uni-rostock.deProkaryotic model organisms E.coli (Escherichia coli)Methanococcus jannaschii (archaeon) Mycoplasma genitalium (simplest organism known) Ulf Schmitz, Introduction to genomics and proteomics I 19
    • www. .uni-rostock.deGenomics • DNA of higher organisms is organized into chromosomes (human – 23 chromosome pairs) • not all DNA codes for proteins • on the other hand some genes exist in multiple copies • that’s why from the genome size you can’t easily estimate the amount of protein sequence information Ulf Schmitz, Introduction to genomics and proteomics I 20
    • www. .uni-rostock.deGenomes of eukaryotes • majority of the DNA is in the nucleus, separated into bundles (chromosomes) – small amounts of DNA appear in organelles (mitochondria and chloroplasts) • within single chromosomes gene families are common – some family members are paralogues (related) • they have duplicated within the same genome • often diverged to provide separate functions in descendants (Nachkommen) • e.g. human α and β globin – orthologues genes • are homologues in different species • often perform the same function • e.g. human and horse myoglobin – pseudogenes • lost their function • e.g. human globin gene cluster pseudogene Ulf Schmitz, Introduction to genomics and proteomics I 21
    • www. .uni-rostock.deEukaryotic model organisms• Saccharomyces cerevisiae (baker’s yeast)• Caenorhabditis elegans (C.elegans)• Drosophila melanogaster (fruit fly)• Arabidopsis thaliana (flower)• Homo sapiens (human) Ulf Schmitz, Introduction to genomics and proteomics I 22
    • www. .uni-rostock.deThe human genome • ~3.2 x 109 bp (thirty time larger than C.elegans or D.melongaster) • coding sequences form only 5% of the human genome • Repeat sequences over 50% • Only ~32.000 genes • Human genome is distributed over 22 chromosome pairs plus X and Y chromosomes • Exons of protein-coding genes are relatively small compared to other known eukaryotic genomes • Introns are relatively long • Protein-coding genes span long stretches of DNA (dystrophin, coding a 3.685 amino acid protein, is >2.4Mbp long) • Average gene length: ~ 8,000 bp • Average of 5-6 exons/gene • Average exon length: ~200 bp • Average intron length: ~2,000 bp • ~8% genes have a single exon • Some exons can be as small as 1 or 3 bp. Ulf Schmitz, Introduction to genomics and proteomics I 23
    • www. .uni-rostock.deThe human genomeTop categories in a function classification: Function Number % Function Number % Nucleic acid binding 2207 14.0 Apoptosis inhibitor 132 0.8 DNA binding 1656 10.5 Signal transduction 1790 11.4 DNA repair protein 45 0.2 Receptor 1318 8.4 DNA replication factor 7 0.0 Transmembrane receptor 1202 7.6 Transcription factor 986 6.2 G-protein link receptor 489 3.1 RNA binding 380 2.4 Olfactory receptor 71 0.0 Structural protein of ribosome 137 0.8 Storage protein 7 0.0 Translation factor 44 0.2 Cell adhesion 189 1.2 Transcription factor binding 6 0.0 Cell Cycle regulator 75 0.4 Structural protein 714 4.5 Cytoskeletal structural protein 145 0.9 Chaperone 154 0.9 Transporter 682 4.3 Motor 85 0.5 Ion channel 269 1.7 Actin binding 129 0.8 Neurotransmitter transporter 19 0.1 Defense/immunity protein 603 3.8 Ligand binding or carrier 1536 9.7 Electron transfer 33 0.2 Enzyme 3242 20.6 Cytochrome P450 50 0.3 Peptidase 457 2.9 Endopeptidase 403 2.5 Tumor suppressor 5 0.0 Protein kinase 839 5.3 Unclassified 30.6 4813 Protein phosphatase 295 1.8 Enzyme activator 3 0.0 Total 15683 100.0 Ulf Schmitz, Introduction to genomics and proteomics I 24
    • www. .uni-rostock.deThe human genome • Repeated sequences comprise over 50% of the genome: – Transposable elements, or interspersed repeats include LINEs and SINEs (almost 50%) – Retroposed pseudogenes – Simple ‘stutters’ - repeats of short oligomers (minisatellites and microsatellites) – Segment duplication, of blocks of ~10 - 300kb – Blocks of tandem repeats, including gene families Copy Fraction of Element Size (bp) number genome % Short Interspersed Nuclear 100-300 1.500.000 13 Elements (SINEs) Long Interspersed Nuclear 6000-8000 850.000 21 Elements (LINEs) Long Terminal Repeats 15.000 -110.000 450.000 8 DNA Transposon fossils 80-3000 300.000 3 Ulf Schmitz, Introduction to genomics and proteomics I 25
    • www. .uni-rostock.deThe human genome• All people are different, but the DNA of different people only varies for 0.2% or less.• So, only up to 2 letters in 1000 are expected to be different.• Evidence in current genomics studies (Single Nucleotide Polymorphisms or SNPs) imply that on average only 1 letter out of 1400 is different between individuals.• means that 2 to 3 million letters would differ between individuals. Ulf Schmitz, Introduction to genomics and proteomics I 26
    • www. .uni-rostock.deFunctional GenomicsFrom gene to function Genome Expressome Proteome TERTIARY STRUCTURE (fold) TERTIARY STRUCTURE (fold) Metabolome Ulf Schmitz, Introduction to genomics and proteomics I 27
    • www. .uni-rostock.deDNA makes RNA makes Protein:Expression data• More copies of mRNA for a gene leads to more protein• mRNA can now be measured for all the genes in a cell at ones through microarray technology• Can have 60,000 spots (genes) on a single gene chip• Color change gives intensity of gene expression (over- or under-expression) Ulf Schmitz, Introduction to genomics and proteomics I 28
    • www. .uni-rostock.deUlf Schmitz, Introduction to genomics and proteomics I 29
    • www. .uni-rostock.deGenes and regulatory regionsregulatory mechanisms organize theexpression of genes – genes may be turned on or off in response to concentrations of nutrients or to stress – control regions often lie near the segments coding for proteins – they can serve as binding sites for molecules that transcribe the DNA – or they bind regulatory molecules that can block transcription Ulf Schmitz, Introduction to genomics and proteomics I 30
    • www. .uni-rostock.deExpression data Ulf Schmitz, Introduction to genomics and proteomics I 31
    • www. .uni-rostock.deOutlook – coming lectureProteomics – Proteins – post-translational modification – Key technologies• Maps of hereditary information• SNPs (Single nucleotide polymorphisms)• Genetic diseases Ulf Schmitz, Introduction to genomics and proteomics I 32
    • www. .uni-rostock.deThanks for your attention! Ulf Schmitz, Introduction to genomics and proteomics I 33
    • www. .uni-rostock.de Bioinformatics Introduction to genomics and proteomics II ulf.schmitz@informatik.uni-rostock.deBioinformatics and Systems Biology Group www.sbi.informatik.uni-rostock.de Ulf Schmitz, Introduction to genomics and proteomics II 1
    • www. .uni-rostock.deOutline1. Proteomics • Motivation • Post -Translational Modifications • Key technologies • Data explosion2. Maps of hereditary information3. Single nucleotide polymorphisms Ulf Schmitz, Introduction to genomics and proteomics II 2
    • www. .uni-rostock.deProtomics Proteomics: • is the large-scale study of proteins, particularly their structures and functions • This term was coined to make an analogy with genomics, and is often viewed as the "next step", • but proteomics is much more complicated than genomics. • Most importantly, while the genome is a rather constant entity, the proteome is constantly changing through its biochemical interactions with the genome. • One organism will have radically different protein expression in different parts of its body and in different stages of its life cycle. Proteome: The entirety of proteins in existence in an organism are referred to as the proteome. Ulf Schmitz, Introduction to genomics and proteomics II 3
    • www. .uni-rostock.deProteomicsIf the genome is a list of the instruments in an orchestra, theproteome is the orchestra playing a symphony.R.Simpson Ulf Schmitz, Introduction to genomics and proteomics II 4
    • www. .uni-rostock.deProteomics• Describing all 3D structures of proteins in the cell is called Structural Genomics• Finding out what these proteins do is called Functional Genomics DNA Microarray GENOME Genetic Screens PROTEOME Protein – Ligand Protein – Protein Interactions Interactions Structure Ulf Schmitz, Introduction to genomics and proteomics II 5
    • www. .uni-rostock.deProteomicsMotivation: • What kind of data would we like to measure? • What mature experimental techniques exist to determine them? • The basic goal is a spatio-temporal description of the deployment of proteins in the organism. Ulf Schmitz, Introduction to genomics and proteomics II 6
    • www. .uni-rostock.deProteomicsThings to consider:• the rates of synthesis of different proteins vary among different tissues and different cell types and states of activity• methods are available for efficient analysis of transcription patterns of multiple genes• because proteins ‘turn over’ at different rates, it is also necessary to measure proteins directly• the distribution of expressed protein levels is a kinetic balance between rates of protein synthesis and degradation Ulf Schmitz, Introduction to genomics and proteomics II 7
    • www. .uni-rostock.deUlf Schmitz, Introduction to genomics and proteomics II 8
    • www. .uni-rostock.deWhy do Proteomics?• are there differences between amino acid sequences determined directly from proteins and those determined by translation from DNA? – pattern recognition programs addressing this questions have following errors: • a genuine protein sequence may be missed entirely • an incomplete protein may be reported • a gene may be incorrectly spliced • genes for different proteins may overlap • genes may be assembled from exons in different ways in different tissues – often, molecules must be modified to make a mature protein that differs significantly from the one suggested by translation • in many cases the missing post-translational- modifications are quite important and have functional significance • post-transitional modifications include addition of ligands, glycosylation, methylation, excision of peptides, etc. – in some cases mRNA is edited before translation, creating changes in the amino acid sequence that are not inferrable from the genes• a protein inferred from a genome sequence is a hypothetical object until an experiment verifies its existence Ulf Schmitz, Introduction to genomics and proteomics II 9
    • www. .uni-rostock.dePost-translational modification• a protein is a polypeptide chain composed of 20 possible amino acids• there are far fewer genes that code for proteins in the human genome than there are proteins in the human proteome (~33,000 genes vs ~200,000 proteins).• each gene encodes as many as six to eight different proteins – due to post-translational modifications such as phosphorylation, glycosylation or cleavage (Spaltung)• posttranslational modification extends the range of possible functions a protein can have – changes may alter the hydrophobicity of a protein and thus determine if the modified protein is cytosolic or membrane-bound – modifications like phosphorylation are part of common mechanisms for controlling the behavior of a protein, for instance, activating or inactivating an enzyme. Ulf Schmitz, Introduction to genomics and proteomics II 10
    • www. .uni-rostock.dePost-translational modification Phosphorylation • phosphorylation is the addition of a phosphate (PO4) group to a protein or a small molecule (usual to serine, tyrosine, threonine or histidine) • In eukaryotes, protein phosphorylation is probably the most important regulatory event • Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation • Phosphorylation is catalyzed by various specific protein kinases, whereas phosphatases dephosphorylate. Acetylation • Is the addition of an acetyl group, usually at the N-terminus of the protein Farnesylation • farnesylation, the addition of a farnesyl group Glycosylation • the addition of a glycosyl group to either asparagine, hydroxylysine, serine, or threonine, resulting in a glycoprotein Ulf Schmitz, Introduction to genomics and proteomics II 11
    • www. .uni-rostock.deProteomics Ulf Schmitz, Introduction to genomics and proteomics II 12
    • www. .uni-rostock.deKey technologies for proteomics 1. 1-D electrophoresis and 2-D electrophoresis • are for the separation and visualization of proteins. 2. mass spectrometry, x-ray crystallography, and NMR (Nuclear magnetic resonance ) • are used to identify and characterize proteins 3. chromatography techniques especially affinity chromatography • are used to characterize protein-protein interactions. 4. Protein expression systems like the yeast two- hybrid and FRET (fluorescence resonance energy transfer) • can also be used to characterize protein-protein interactions. Ulf Schmitz, Introduction to genomics and proteomics II 13
    • www. .uni-rostock.de Key technologies for proteomics High-resolution two-dimensional polyacrylamide gel electrophoresis (2D PAGE) shows the pattern of protein content in a sample.Reference map of lympphoblastoidcell linePRI, soluble proteins.• 110 µg of proteins loaded• Strip 17cm pH gradient 4-7, SDS PAGE gels 20 x 25 cm, 8-18.5% T.• Staining by silver nitrate method (Rabilloud et al.,)• Identification by mass spectrometry. The pinks labels on the spots indicate the ID in Swiss-prot database browse the SWISS-2DPAGE database for more 2d PAGE images Ulf Schmitz, Introduction to genomics and proteomics II 14
    • www. .uni-rostock.deProteomicsX-ray crystallography is a means todetermine the detailed molecularstructure of a protein, nucleic acid orsmall molecule.With a crystal structure we can explain themechanism of an enzyme, the binding of aninhibitor, the packing of protein domains, thetertiary structure of a nucleic acid moleculeetc..Typically, a sample is purified tohomogeneity, crystallized, subjected to an X-ray beam and diffraction data are collected. Ulf Schmitz, Introduction to genomics and proteomics II 15
    • www. .uni-rostock.deHigh-throughput Biological Data • Enormous amounts of biological data are being generated by high-throughput capabilities; even more are coming – genomic sequences – gene expression data (microarrays) – mass spec. data – protein-protein interaction (chromatography) – protein structures (x-ray christallography) – ...... Ulf Schmitz, Introduction to genomics and proteomics II 16
    • www. .uni-rostock.deProtein structural data explosionProtein Data Bank (PDB): 33.367 Structures (1 November 2005)28.522 x-ray crystallography, 4.845 NMR Ulf Schmitz, Introduction to genomics and proteomics II 17
    • www. .uni-rostock.deMaps of hereditary information Following maps are used to find out how hereditary information is stored, passed on, and implemented. 1. Linkage maps of genes mini- / microsatellites 2. Banding patterns of chromosomes physical objects with visible landmarks called banding patterns 3. DNA sequences Contig maps (contigous clone maps) Sequence tagged site (STS) SNPs (Single nucloetide polymorphisms) Ulf Schmitz, Introduction to genomics and proteomics II 18
    • www. .uni-rostock.deLinkage map Ulf Schmitz, Introduction to genomics and proteomics II 19
    • www. .uni-rostock.deMaps of hereditary informationVariable number tandem repeats (VNTRs, also minisatellites)• regions, 8-80bp long, repeated a variable number of times• the distribution and the size of repeats is the marker• inheritance of VNTRs can be followed in a family and mapped to a pathological phenotype• first genetic data used for personal identification – Genetic fingerprints; in paternity and in criminal casesShort tandem repeat polymorphism (STRPs, also microsatellites) • Regions of 2-7bp, repeated many times – Usually 10-30 consecutive copies Ulf Schmitz, Introduction to genomics and proteomics II 20
    • www. .uni-rostock.de centromere3bpCGTCGTCGTCGTCGTCGTCGTCGT...GCAGCAGCAGCAGCAGCAGCAGCA... Ulf Schmitz, Introduction to genomics and proteomics II 21
    • www. .uni-rostock.deMaps of hereditary informationBanding patterns ofchromosomes Ulf Schmitz, Introduction to genomics and proteomics II 22
    • www. .uni-rostock.deMaps of hereditary information Banding patterns of chromosomes petite – arm centromere queue - arm Ulf Schmitz, Introduction to genomics and proteomics II 23
    • www. .uni-rostock.deMaps of hereditary information Contig map (also contiguous clone map)• Series of overlapping DNA clones of known order along a chromosome from an organism of interest, stored in yeast or bacterial cells as YACs (Yeast Artificial Chromosomes) or BACs (Bacterial Artificial Chromosomes)• A contig map produces a fine mapping (high resolution) of a genome• YAC can contain up to 106bp, a BAC about 250.000bp Sequence tagged site (STS)• Short, sequenced region of DNA, 200-600bp long, that appears in a unique location in the genome• One type arises from an EST (expressed sequence tag), a piece of cDNA Ulf Schmitz, Introduction to genomics and proteomics II 24
    • www. .uni-rostock.deMaps of hereditary informationImagine we know that a disease results from a specificdefective protein: 1. if we know the protein involved, we can pursue rational approaches to therapy 2. if we know the gene involved, we can devise tests to identify sufferers or carriers 3. wereas the knowledge of the chromosomal location of the gene is unnecessary in many cases for either therapy or detection; • it is required only for identifying the gene, providing a bridge between the patterns of inheritance and the DNA sequence Ulf Schmitz, Introduction to genomics and proteomics II 25
    • www. .uni-rostock.deSingle nucleotide polymorphisms (SNPs)• SNP (pronounced ‘snip’) is a genetic variation between individuals• single base pairs that can be substituted, deleted or inserted• SNPs are distributed throughout the genome – average every 2000bp• provide markers for mapping genes• not all SNPs are linked to diseases Ulf Schmitz, Introduction to genomics and proteomics II 26
    • www. .uni-rostock.deSingle nucleotide polymorphisms (SNPs) • nonsense mutations: – codes for a stop, which can truncate the protein • missense mutations: – codes for a different amino acid • silent mutations: – codes for the same amino acid, so has no effect Ulf Schmitz, Introduction to genomics and proteomics II 27
    • www. .uni-rostock.deOutlook – coming lecture• Bioinformatics Information Resources And Networks – EMBnet – European Molecular Biology Network • DBs and Tools – NCBI – National Center For Biotechnology Information • DBs and Tools – Nucleic Acid Sequence Databases – Protein Information Resources – Metabolic Databases – Mapping Databases – Databases concerning Mutations – Literature Databases Ulf Schmitz, Introduction to genomics and proteomics II 28
    • www. .uni-rostock.deThanks for your attention! Ulf Schmitz, Introduction to genomics and proteomics II 29