Biological Sequence Analysis

Spring 2008

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Teachers:Nimrod Rubinstein rubi@post.tau.ac.ilDudu Burstein davidbur@post.tau.ac.il

Tel: 03-640-9245

Reception hours:by appointment.

Course website:

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Administration

http://bioinfo.tau.ac.il/~intro_bioinfo/mta

Requirements1: Introduction

•Home assignments – 25%

•Midterm quiz – 25%

•Final project – 50%

All assignments must be submitted on time

Do not copy!

Goals

To familiarize the students with research topics in sequence analysis in bioinformatics, and with relevant tools in this field

Prerequisites

• Familiarity with topics in molecular biology (cell biology and genetics)

• Basic familiarity with computers & internet

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Ask, Ask, Ask!!

"אין הביישן למד"

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What is Bioinformatics

• “The analysis of biological information using computers and statistical techniques; the science of developing and utilizing computer databases and algorithms to accelerate and enhance biological research “

www.niehs.nih.gov/dert/trc/glossary.htm

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What do bioinformaticians study?

• Bioinformatics today is part of almost every molecular biological research

• To name a few examples…

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Example 1

• Compare proteins with similar sequences (for instance –kinases) and understand what the similarities and differences mean

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Example 2

• Look at the genome and predict where genes are located (promoters; transcription factor binding sites; introns; exons)

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• Predict the 3-dimensional structure of a protein from its primary sequence

Example 3

Ab-initio prediction – extremely difficult!

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• Correlate between gene expression and disease

Example 4

A gene chip – quantifying gene expression in different tissues under different conditions

May be used for personalized medicine

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Computational biology – revolutionizing science at the turn of the century

Three studies using bioinformatics which highly impacted science

1. Classifying life into domains2. Predicting drug resistance in HIV

and personalizing drug administration

3. Solving the mystery of anthrax molecular biology

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1. Revolutionizing the Classification of Life

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•Life was classified as

plants and animals

•When Bacteria were discoveredthey were initially classified as plants

•Ernst Haeckel (1866) placed all unicellular organisms in a kingdom called Protista, separated from Plantae and Animalia

In the very beginning

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Thus, life were classified to 5 kingdoms:

When electron microscopes were developed, it was found that Protista in fact include both cells with and without nucleus. Also, fungi were found to differ from plants, since they are heterotrophs (they do not synthesize their food)

LIFE

FungiPlants Animals ProtistsProcaryotes

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Later on, plants, animals, protists and fungi were collectively called the Eucarya domain, and the procaryotes were shifted from a kingdom to be a Bacteria domain

Domains EucaryaBacteria

FungiPlants Animals ProtistsKingdoms

Even later, a new Domain was discovered…

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•The translation apparatus is universal and probably already existed in the “beginning”

rRNA was sequenced from a great number of organisms to study phylogeny

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Carl R. Woese and rRNA phylogeny1: Introduction

A distance matrix was computed for each two organisms. In a very influential paper, they showed that methanogenic bacteria are as distant from bacteria as they are from eucaryota (1977)

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One sentence about methanogenic “bacteria”

“There exists a third kingdom which, to date, is represented solely by the methanogenic bacteria, a relatively unknown class of anaerobes that possess a unique metabolism based on the reduction of carbon dioxide to methane”.

These "bacteria" appear to be no more related to typical bacteria than they are to eucaryotic cytoplasms.“

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From sequence analysis only, it was thus established that life is divided into 3 domains:BacteriaArchaeaEucarya

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The rRNA phylogenetic tree

2. Revolutionizing HIV treatment

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There are very efficient drugs for AIDS treatment

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A few viruses in blood

DRUG, +a few more days

Many viruses in blood

DRUG, +a few days

Many viruses in blood

Explanation: the virus mutates and some viruses become resistant to the drug

Solution 1: combination of drugs (cocktail)

Solution 2: not to give drugs for which the virus is already resistant. For example, if one was infected from a person who receives a specific drug.

The question: how does one know to which drugs the virus is already resistant?

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Sequences of HIV-1 from patients who were treated with drug A:

AAGACGCATCGATCGATCGATCGTACGACGACGCATCGATCGATCGATCGTACGAAGACACATCGATCGTTCGATCGTACG

Sequences of HIV-1 from patients who were never treated with drug A:AAGACGCATCGATCGATCGATCTTACGAAGACGCATCGATCGATCGATCTTACG AAGACGCATCGATCGATCGATCTTACG

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drug A+AAGACGCATCGATCGATCGATCGTACGACGACGCATCGATCGATCGATCGTACGAAGACACATCGATCGTTCGATCGTACG

drug A-AAGACGCATCGATCGATCGATCTTACGAAGACGCATCGATCGATCGATCTTACG AAGACGCATCGATCGATCGATCTTACG

This is an easy example!

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drug A+AAGACGCATCGATCGATCGATCGTACGACGACGCATCGATCGATCGATCGTACGAAGACACATCGATCATTCGATCATACG

drug A-AAGACGCATCGATCTATCGATCTTACGAAGACGCATCGATCTATCGATCTTACG AAGACGCATCGATCAATCGATCGTACG

This is NOT an easy example! It’s an example of a classification problem

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2006: Five machine learning tools were compared:•Decision trees•Linear regression•Linear discriminant analysis•Neural networks•Support vector regression

~80% accuracy

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3. Revolutionizing our understanding of the anthrax molecular mechanism

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•Anthrax is a disease whose causative agent is the gram positive Bacillus anthracis

•It infects mainly cattle, swine, and horses but it can also infect humans

•Humans are infected from milk or meat from infected animals

•In humans, it causes skin problems, in cattle – fatal blood poisoning

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•A vaccine was found by Pasteur

•Koch was the first to isolate the bacterium

•Airborne anthrax, such as that induced by weaponized strains used forbioterrosrism is almost always fatal in humans (respiratory distress, hemorrhage)

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How does the bacterium Bacillus anthracis work?It secretes three proteins: protective antigen (PA), edema factor (EF), and lethal factor (LF)

PA monomer first binds to a host-cell surface receptor. This binding triggers proteolytic cleavage (a part of the N terminus is cut out)

The (remaining) PA monomers oligomerize, forming heptamers

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LF and EF bind the heptamer and the entire complex is internalized into an endosome

The acidity in the endosome causes a conformational change in the complex, which helps it penetrate the endosome membrane and to form a pore

The story continues…

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Researchers from the group of David Baker wanted to know how LF and EF bind to the heptameric PA. They used a bioinformatics method called docking…

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This is where the two proteins interact!

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Once they had a prediction, they performed mutagenesis experiments. Changing residues in the predicted interface cancelled the binding interaction.

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How does docking work? Each 3D conformation is given a score. The pair with the best score is chosen

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Challenges: what is the best score?How to go over as many conformations as possible?How to take into account that proteins are flexible?

Gregor Mendellaws of inheritance,“gene”1866

Watson and Crick

DNA Discovery 1953

Genome

Project 2003

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Genomics: historical chronicle

Genome

Project 2003

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)Slide from Prof. Ron Shamir(

BioinformaticsBioinformatics

• Organize, store, analyze, visualize genomic data • Utilizes methods from Computer Science,

Mathematics, Statistics and Biology

The marriage of Computer Science and Biology

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)Slide from Prof. Ron Shamir(

• At the convergence of two revolutions: the ultra-fast growth of biological data, and the information revolution

Biology is becoming an information science

22 Aug 2005:100,000,000,000 bases

1: Introduction Bioinformatics)Slide from Prof. Ron Shamir(

Bioinformatics – a short CV

• Born ~1990• Grown rapidly• Experience: essential part of modern

Biomedical sciences• Now, a separate multidisciplinary scientific

area• Is one of the cornerstones of 21st Century

biomedical research

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)Slide from Prof. Ron Shamir(

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•Academic research: where it all started•Biotechnology companies•Big Pharmas•National and international centers

The Bioinformatics Actors

Find me gene (gin?)

Bioinformatics in Israel

• World class player in research

• Ranked 2-3 in absolute number of papers in the most prestigious and competitive conferences

• Maintaining our competitive global position is nontrivial

1: Introduction )Slide from Prof. Ron Shamir(