1 Introduction to Bioinformatics Esa Pitkänen [email protected]Autumn 2008, I period www.cs.helsinki.fi/mbi/courses/08-09/itb 582606 Introduction to Bioinformatics, Autumn 2008 Introduction to Bioinformatics Lecture 1: Administrative issues MBI Programme, Bioinformatics courses What is bioinformatics? Molecular biology primer 3 How to enrol for the course? p Use the registration system of the Computer Science department: https://ilmo.cs.helsinki.fi n You need your user account at the IT department (“cc account”) p If you cannot register yet, don’t worry: attend the lectures and exercises; just register when you are able to do so 4 Teachers p Esa Pitkänen, Department of Computer Science, University of Helsinki p Elja Arjas, Department of Mathematics and Statistics, University of Helsinki p Sami Kaski, Department of Information and Computer Science, Helsinki University of Technology p Lauri Eronen, Department of Computer Science, University of Helsinki (exercises) 5 Lectures and exercises p Lectures: Tuesday and Friday 14.15-16.00 Exactum C221 p Exercises: Tuesday 16.15-18.00 Exactum C221 n First exercise session on Tue 9 September 6 Status & Prerequisites p Advanced level course at the Department of Computer Science, U. Helsinki p 4 credits p Prerequisites: n Basic mathematics skills (probability calculus, basic statistics) n Familiarity with computers n Basic programming skills recommended n No biology background required
14
Embed
Introduction to Bioinformatics Introduction to Bioinformatics -
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Bioinformatics courses in Helsinkiregion: 3rd periodp Evolution and the theory of games (5 credits, Kumpula)p Genome-wide association mapping (6-8 credits, Kumpula)p High-Throughput Bioinformatics (5-7 credits, TKK)p Image Analysis in Neuroinformatics (5 credits, TKK)p Practical Course in Biodatabases (4-5 credits, Kumpula)p Seminar: Computational systems biology (3 credits,
Kumpula)p Spatial models in ecology and evolution (8 credits,
Kumpula)p Special course in bioinformatics I (3-7 credits, TKK)
23
Bioinformatics courses in Helsinki region:4th periodp Metabolic Modeling (4 credits, Kumpula)p Phylogenetic data analyses (6-8 credits,
What is bioinformatics?p Bioinformatics, n. The science of information
and information flow in biological systems,esp. of the use of computational methods ingenetics and genomics. (Oxford EnglishDictionary)
p "The mathematical, statistical and computingmethods that aim to solve biological problemsusing DNA and amino acid sequences andrelated information." -- Fredj Tekaia
26
What is bioinformatics?p "I do not think all biological computing is
bioinformatics, e.g. mathematical modelling isnot bioinformatics, even when connected withbiology-related problems. In my opinion,bioinformatics has to do with management andthe subsequent use of biological information,particular genetic information."-- Richard Durbin
27
What is not bioinformatics?p Biologically-inspired computation, e.g., genetic algorithms
and neural networksp However, application of neural networks to solve some
biological problem, could be called bioinformaticsp What about DNA computing?
Computational biologyp Application of computing to biology (broad
definition)p Often used interchangeably with bioinformaticsp Or: Biology that is done with computational
means
29
Biometry & biophysicsp Biometry: the statistical analysis of biological
datan Sometimes also the field of identification of individuals
using biological traits (a more recent definition)
p Biophysics: "an interdisciplinary field whichapplies techniques from the physical sciencesto understanding biological structure andfunction" -- British Biophysical Society
30
Mathematical biologyp Mathematical biology
“tackles biologicalproblems, but the methodsit uses to tackle them neednot be numerical and neednot be implemented insoftware or hardware.”-- Damian Counsell
Turing on biological complexityp “It must be admitted that the biological examples which
it has been possible to give in the present paper are verylimited.
This can be ascribed quite simply to the fact thatbiological phenomena are usually very complicated.Taking this in combination with the relatively elementarymathematics used in this paper one could hardly expect tofind that many observed biological phenomena would becovered.
It is thought, however, that the imaginary biologicalsystems which have been treated, and the principles whichhave been discussed, should be of some help ininterpreting real biological forms.”
– Alan Turing, The Chemical Basis of Morphogenesis, 1952
32
Related conceptsp Systems biology
n “Biology of networks”n Integrating different levels
of information tounderstand how biologicalsystems work
p Computational systems biology
Overview of metabolic pathways inKEGG database, www.genome.jp/kegg/
33
Why is bioinformatics important?p New measurement techniques produce
huge quantities of biological datan Advanced data analysis methods are needed to
make sense of the datan Typical data sources produce noisy data with a
lot of missing values
p Paradigm shift in biology to utilisebioinformatics in research
34
Bioinformatician’s skill setp Statistics, data analysis methods
n Lots of datan High noise levels, missing valuesn #attributes >> #data points
p Programming languagesn Scripting languages: Python, Perl, Ruby, …n Extensive use of text file formats: need
parsersn Integration of both data and tools
p Data structures, databases
35
Bioinformatician’s skill setp Modelling
n Discrete vs continuous domainsn -> Systems biology
p Scientific computation packagesn R, Matlab/Octave, …
p Communication skills!
36
Communication skills: case 1Biologist presents a problemto computer scientists /mathematicians
?
”I am interested in finding what affects theregulation gene x during condition y and how
Mathematics andstatistics• Calculus• Probability calculus• Linear algebra
Biology & Medicine• Basics in molecular andcell biology• Measurement techniques
Bioinformatics• Biological sequence analysis• Biological databases• Analysis of gene expression• Modeling protein structure andfunction• Gene, protein and metabolicnetworks• …
Bioinformatician’s skill set
Prof. Juho Rousu, 2006
Where would you be in this triangle?
42
A problem involving bioinformatics?
- ”I found a fruit fly that is immune to all diseases!”
Molecular Biology Primer by Angela Brooks, Raymond Brown,Calvin Chen, Mike Daly, Hoa Dinh, Erinn Hama, Robert Hinman,Julio Ng, Michael Sneddon, Hoa Troung, Jerry Wang, Che FungYungEdited for Introduction to Bioinformatics (Autumn 2007, Summer2008, Autumn 2008) by Esa Pitkänen 44
Molecular biology primerp Part 1: What is life made of?p Part 2: Where does the variation in
genomes come from?
45
Life begins with Cell
p A cell is a smallest structural unit of anorganism that is capable of independentfunctioning
p All cells have some common features
46
Cellsp Fundamental working units of every living system.p Every organism is composed of one of two radically different types of
cells:n prokaryotic cells orn eukaryotic cells.
p Prokaryotes and Eukaryotes are descended from the sameprimitive cell.n All prokaryotic and eukaryotic cells are the result of a total of 3.5
billion years of evolution.
47
Two types of cells: Prokaryotes andEukaryotes
48
Prokaryotes and Eukaryotesp According to the most
recent evidence, thereare three mainbranches to the tree oflife
p Prokaryotes includeArchaea (“ancientones”) and bacteria
p Eukaryotes arekingdom Eukarya andincludes plants,animals, fungi andcertain algae Lecture: Phylogenetic trees
9
49
All Cells have common Cycles
p Born, eat, replicate, and die
50
Common features of organismsp Chemical energy is stored in ATPp Genetic information is encoded by DNAp Information is transcribed into RNAp There is a common triplet genetic codep Translation into proteins involves ribosomesp Shared metabolic pathwaysp Similar proteins among diverse groups of
organisms
51
All Life depends on 3 critical moleculesp DNAs (Deoxyribonucleic acid)
n Hold information on how cell works
p RNAs (Ribonucleic acid)n Act to transfer short pieces of information to different
parts of celln Provide templates to synthesize into protein
p Proteinsn Form enzymes that send signals to other cells and
regulate gene activityn Form body’s major components (e.g. hair, skin, etc.)n “Workhorses” of the cell
52
DNA: The Code of Life
p The structure and the four genomic letters code for all livingorganisms
p Adenine, Guanine, Thymine, and Cytosine which pair A-T and C-Gon complimentary strands.
Lecture: Genome sequencingand assembly
53
Discovery of the structure of DNAp 1952-1953 James D. Watson and Francis H. C. Crick
deduced the double helical structure of DNA from X-raydiffraction images by Rosalind Franklin and data on amountsof nucleotides in DNA
James Watson andFrancis Crick
RosalindFranklin
”Photo 51”
54
DNA, continuedp DNA has a double helix
structure which iscomposed ofn sugar moleculen phosphate groupn and a base (A,C,G,T)
p By convention, we readDNA strings in direction oftranscription: from 5’ endto 3’ end5’ ATTTAGGCC 3’3’ TAAATCCGG 5’
RNAp RNA is similar to DNA chemically. It is usually only a
single strand. T(hyamine) is replaced by U(racil)p Several types of RNA exist for different functions in
the cell.
http://www.cgl.ucsf.edu/home/glasfeld/tutorial/trna/trna.giftRNA linear and 3D view:
60
DNA, RNA, and the Flow ofInformation
TranslationTranscription
Replication ”The central dogma”
Is this true?
Denis Noble: The principles of Systems Biology illustrated using the virtual hearthttp://velblod.videolectures.net/2007/pascal/eccs07_dresden/noble_denis/eccs07_noble_psb_01.ppt
How DNA/RNA codes for protein?p DNA alphabet contains four
letters but must specifyprotein, or polypeptidesequence of 20 letters.
p Dinucleotides are notenough: 42 = 16 possibledinucleotides
p Trinucleotides (triplets)allow 43 = 64 possibletrinucleotides
p Triplets are also calledcodons
64
How DNA/RNA codes for protein?p Three of the possible
triplets specify ”stoptranslation”
p Translation usually startsat triplet AUG (this codesfor methionine)
p Most amino acids may bespecified by more thantriplet
p How to find a gene? Lookfor start and stop codons(not that easy though)
65
Proteins: Workhorses of the Cell
p 20 different amino acidsn different chemical properties cause the protein chains to fold
up into specific three-dimensional structures that define theirparticular functions in the cell.
p Proteins do all essential work for the celln build cellular structuresn digest nutrientsn execute metabolic functionsn mediate information flow within a cell and among cellular
communities.p Proteins work together with other proteins or nucleic acids
as "molecular machines"n structures that fit together and function in highly specific, lock-
and-key ways.
Lecture 8: Proteomics
66
Genesp “A gene is a union of genomic sequences encoding a
coherent set of potentially overlapping functional products”--Gerstein et al.
p A DNA segment whose information is expressed either asan RNA molecule or protein