BME280/CSE277/CSE377: BioinformaticsSpring 2006

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Administrivia

• Lecture time: TTh 12:30-1:45pm• Lecture place: Engineering II, Room 322• Instructor: Ion Mandoiu

– Office: ITEB 261– Tel: 6-3784– E-mail: ion@engr.uconn.edu– Office hours: MW 1-2pm

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Textbooks

• Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT Press, 2004. Textbook website: http://bioalgorithms.info/. (REQUIRED)

• D. Gusfield, Algorithms on Strings, Trees, and Sequences, Cambridge University Press, 1997 (OPTIONAL)

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Grading

• 30% homework assignments– Bi-weekly

• 30% programming projects– Individual, 3-4 projects

• 40% final project– Individual or teams of 2– Written report + short presentation– Possible topics

• Algorithm implementation + empirical study• In-depth survey of a topic not covered in class• Progress on open research problems• Propose your own!

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What is Bioinformatics?

• Bioinformatics is generally defined as the analysis, prediction, and modeling of biological data with the help of computers

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Why Bioinformatics?

• DNA sequencing technologies have created massive amounts of information that can only be efficiently analyzed with computers

• Hundreds of species sequenced– Human, rat, chimp, chicken, …

• As the information becomes ever so larger and more complex, more computational tools are needed to sort through the data. – Biology is becoming an information science!

– Slowly, we are learning how cells work through comparative genomics -- not unlike comparative linguistics

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Bioinformatics Tools

• Bioinformatics problems involve multiple aspects– Example: Sequence Comparison

• Biology: How are genes evolving? How is gene function related to gene sequence?

• Learning/AI: How do we define “similar’’? Can we learn from examples?

• Algorithms: How can we efficiently find all similar sequences?• Statistics: How do we distinguish a random match from a true

one?

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Course Description

• Course emphasis– Modeling computational problems arising in biology as graph-theoretic,

statistical, or mathematical optimization problems– Design, analysis, and implementation of efficient algorithms

• Algorithmic techniques to be covered– Exhaustive search– Integer programming– Greedy algorithms– Dynamic programming– Divide-and-conquer– Graph algorithms– Combinatorial pattern matching– Clustering– Hidden Markov models– Randomized algorithms

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Course Description

• Biological applications – Restriction mapping– DNA sequencing– Motif finding– Pairwise sequence alignment– Gene prediction– Evolutionary trees– Genome rearrangements

Complete and return the survey!

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Basic Molecular Biology

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The Cell

Source: D. Geiger

All cells contain the same DNA, yet there are many types of cells!

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Mendel and his Genes

• Genes -- physical and functional traits passed on from one generation to the next

• Discovered by Gregor Mendel in the 1860s while he was experimenting with the pea plant. He asked the question:

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The Pea Plant Experiments

• Mendel discovered that genes were passed on to offspring by both parents in two forms: dominant and recessive.

• The dominant form would be the phenotypic characteristic of the offspring

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DNA: The Code of Life

• The structure and the four genomic letters code for all living organisms • Adenine, Guanine, Thymine, and Cytosine which pair A-T and C-G on

complimentary strands.

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DNA Components

Source: D. Geiger

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The Human Genome

Source: D. Geiger

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DNA Organization

Source: D. Geiger

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Genome Sizes

• E. Coli (bacteria) 4.7 Mb (Mega bases)

• Yeast (simple fungi) 15 Mb• Nematode (C. Elegans) 100 Mb• Mouse 2 Gb (Giga bases)• Human 3 Gb• Wheat 16.5 Gb• Lily 32-48 Gb

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Genes

• DNA strings contain:– Coding regions (genes)– Control regions– “Junk” DNA (unknown function)

• Estimated number of genes:– E. Coli (bacteria) 4,000– Yeast (simple fungi) 6,000– Nematode (C. Elegans) 13,000– Human 32,000 (?)

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Central Dogma

• Cells express different subsets of genes under different environments

Gene

mRNAProtein

Transcription Translation

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Gene Transcription

Source: D. GeigerRNA: similar to DNA, but has

• slightly different backbone

• Uracil (U) instead of Thymine (T)

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RNA Roles

Source: D. Geiger

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Translation

• Catalyzed by Ribosome• Using two different sites, the

Ribosome continually binds tRNA, joins the amino acids together and moves to the next location along the mRNA

• ~10 codons/second, but multiple translations can occur simultaneously

http://wong.scripps.edu/PIX/ribosome.jpg

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Genetic Code

Source: D. Geiger

• Human cells produce approx. 100,000 proteins

• Proteins are poly-peptides consisting of 70-3,000 amino acids

• There are 20 different amino acids; every 3 nucleotides in a gene encode for 1 amino acid (or the STOP signal)

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Protein Folding

• Proteins are not linear structures, though they are built that way

• The amino acids have very different chemical properties; they interact with each other after the protein is built– This causes the protein to start fold and adopting it’s functional

structure– Proteins may fold in reaction to some ions, and several separate

chains of peptides may join together through their hydrophobic and hydrophilic amino acids to form a polymer

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Protein Folding (cont’d)

• The structure that a protein adopts is vital to it’s chemistry

• Its structure determines which of its amino acids are exposed carry out the protein’s function

• Its structure also determines what substrates it can react with

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Protein Structure

Source: D. Geiger

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Basic Molecular Biotechnology

How is information accessed at molecular level?

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• Amplification (making many copies)• Cutting into shorter fragments• Reading fragment lengths• Reading DNA sequence• Probing presence of specific fragments

Operations on DNA/RNA

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Why we need so many copies

• Biologists needed to find a way to read DNA codes.• How do you read base pairs that are angstroms in size?

– It is not possible to directly look at it due to DNA’s small size.

– Need to use chemical techniques to detect what you are looking for.

– To read something so small, you need a lot of it, so that you can actually detect the chemistry.

• Need a way to make many copies of the base pairs, and a method for reading the pairs.

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Polymerase Chain Reaction

• Problem: Modern instrumentation cannot easily detect single molecules of DNA, making amplification a prerequisite for further analysis

• Solution: PCR doubles the number of DNA fragments at every iteration

1… 2… 4… 8…

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Denaturation

Raise temperature to 94oC to separate the duplex form of DNA into single strands

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Design primers

• To perform PCR, a 10-20bp sequence on either side of the sequence to be amplified must be known because DNA pol requires a primer to synthesize a new strand of DNA

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Annealing

• Anneal primers at 50-65oC

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Annealing

• Anneal primers at 50-65oC

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Extension

• Extend primers: raise temp to 72oC, allowing Taq pol to attach at each priming site and extend a new DNA strand

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Extension

• Extend primers: raise temp to 72oC, allowing Taq pol to attach at each priming site and extend a new DNA strand

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Repeat

• Repeat the Denature, Anneal, Extension steps at their respective temperatures…

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Polymerase Chain Reaction

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Restriction Enzymes

• Discovered in the early 1970’s

– Used as a defense mechanism by bacteria to break down the DNA of attacking viruses.

– They cut the DNA into small fragments.

• Can also be used to cut the DNA of organisms.

– This allows the DNA sequence to be in a more manageable bite-size pieces.

• It is then possible using standard purification techniques to single out certain fragments and duplicate them to macroscopic quantities.

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Molecular Scissors

Molecular Cell Biology, 4th editionfig 9-10

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Discovering Restriction Enzymes

• HindII: first restriction enzyme discovered by Hamilton Smith in 1970

– From bacterium Haemophilus influenzae

– Discovered accidentally while studying how the bacterium Haemophilus influenzae takes up DNA from the phage virus P22

– Recognizes and cuts DNA at sequences:

• GTGCAC• GTTAAC

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Recognition Sites of Restriction Enzymes

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Separating DNA by Size

• Gel electrophoresis is a process for separating DNA by size

• Can separate DNA fragments that differ in length in only 1 nucleotide for fragments up to 500 nucleotides long

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Gel Electrophoresis

• DNA fragments are injected into a gel positioned in an electric field

• DNA are negatively charged near neutral pH– The ribose phosphate backbone of each nucleotide is

acidic; DNA has an overall negative charge• DNA molecules move towards the positive electrode

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Gel Electrophoresis (cont’d)

• DNA fragments of different lengths are separated according to size– Smaller molecules move through the gel matrix more

readily than larger molecules• The gel matrix restricts random diffusion so molecules of

different lengths separate into bands

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Detecting DNA: Autoradiography

• One way to visualize separated DNA bands on a gel is autoradiography:

• The DNA is radioactively labeled

• The gel is laid against a sheet of photographic film in the dark, exposing the film at the positions where the DNA is present.

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Detecting DNA: Fluorescence

• Another way to visualize DNA bands in gel is fluorescence:

• The gel is incubated with a solution containing the fluorescent dye ethidium

• Ethidium binds to the DNA

• The DNA lights up when the gel is exposed to ultraviolet light.

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Gel Electrophoresis: Example

Direction of DNA movement

Smaller fragments travel farther

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Sequencing

• Biologists can reliably find the sequence of A/C/T/G for short strings (few hundred nucleotides)

• Chain termination– Single strand template– Complementary strand synthesis blocked with small probability at

particular nucleotides– Lengths of fragments read for each class of strings

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Sequencing

• Biologists can reliably find the sequence of A/C/T/G for short strings (few hundred nucleotides)

• Chain termination– Single strand template– Complementary strand synthesis blocked with small probability at

particular nucleotides– Lengths of fragments read for each class of strings

A C T G----

--------

--------

--------

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Sequencing

• Biologists can reliably find the sequence of A/C/T/G for short strings (few hundred nucleotides)

• Chain termination– Single strand template– Complementary strand synthesis blocked with small probability at

particular nucleotides– Lengths of fragments read for each class of strings

A C T G----

--------

--------

--------

ATACGGAATACGGATACGATACATAATA

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Sequencing

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DNA Hybridization

• Single-stranded DNA will naturally bind to complementary strands

• Hybridization is used to locate genes, regulate gene expression, and determine the degree of similarity between DNA from different sources

• Hybridization is also referred to as annealing or renaturation

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Microarray Technologies

• Oligonucleotide arrays– Short (20-60bp) synthetic DNA strands

• Arrays of cDNAs– Obtained by reverse transcription from Expressed Sequence

Tags (ESTs)

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DNA Array Hybridization Experiment

Images courtesy of Affymetrix.

Tagged RNA fragments flushed over array Laser activation of fluorescent tags

Optical scanning of hybridization

intensities

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Two-Color Technique

• Sample labeled RED• Control labeled GREEN• YELLOWYELLOW probes hybridize to both sample and control•BLACK probes hybridize to neither

Cy3Cy3Cy3

Cy5Cy5Cy5

cell type 2

cell type 1

RNA 2

RNA 1

target 1

target 2

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Sequencing by Hybridization

• Exploits parallel hybridization capabilities offered by DNA arrays

• ALL probes of a certain length k (k=8 to 10) are synthesized on the array

• Target DNA hybridizes at locations which store probes complementary to its k-substrings

• Sequencing by Hybridization (SBH) Problem: Reconstruct target DNA given its k-length substrings (spectrum)

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• Cloning in expression vectors

• 2-Dimensional gel electrophoresis: separate proteins by molecular weight/pH gradient

• Antibody techniques (immunoprecipitation, antibody arrays,…)

• Mass spectrometry (e.g., MALDI-TOF)

• …

Operations on Proteins

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• Genome projects have already given draft genome sequence for hundreds of species, but lots of questions remain to be answered

– Create a complete “parts” list: gene sequences (including intron/exon structure), transcription factors, …

– Understand function of each part, e.g., protein structure, protein/DNA and protein/protein interactions

– Understand mechanisms, e.g., pathways

– Understand how everything fits together: systems biology

Active research problems