CS 5263 Bioinformatics

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CS 5263 Bioinformatics

• Lectures 1 2 Introduction to Bioinformatics
  and Molecular Biology

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Outline

• Administravia
• What is bioinformatics
• Why bioinformatics
• Course overview
• Short introduction to molecular biology

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Survey form

• Your name
• Email
• Academic preparation
• Interests
• help me better design lectures and assignments

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Course Info

• Instructor Jianhua Ruan
• Office S.B. 4.01.48
• Phone [phone]
• Email jruan_at_cs.utsa.edu
• Office hours MW 2-3pm
• Web http//www.cs.utsa.edu/jruan/teaching/cs5263
  _fall_2008/

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Course description

• A survey of algorithms and methods in
  bioinformatics, approached from a computational
  viewpoint.
• Prerequisite
• Programming experiences
• Some knowledge in algorithms and data structures
• Basic understanding of statistics and probability
• Appetite to learn some biology

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Textbooks

• An Introduction to Bioinformatics Algorithms
• by Jones and Pevzner
• Biological Sequence Analysis Probabilistic
  Models of Proteins and Nucleic Acids
• by Durbin, Eddy, Krogh and Mitchison
• Additional resources
• Papers
• Handouts
• See course website

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Grading

• Attendance 10
• At most 2 classes missed without affecting grade
• Homeworks 50
• About 5 assignments
• Combination of theoretical and programming
  exercises
• No exams
• No late submission accepted
• Read the collaboration policy!
• Final project and presentation 40

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Why bioinformatics

• The advance of experimental technology has
  generated huge amount of data
• The human genome is finished
• Even if it were, thats only the beginning
• The bottleneck is how to integrate and analyze
  the data
• Noisy
• Diverse

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Growth of GenBank vs Moores law
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Genome annotations
Meyer, Trends and Tools in Bioinfo and Compt Bio,
2006
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What is bioinformatics

• National Institutes of Health (NIH)
• Research, development, or application of
  computational tools and approaches for expanding
  the use of biological, medical, behavioral or
  health data, including those to acquire, store,
  organize, archive, analyze, or visualize such
  data.

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What is bioinformatics

• National Center for Biotechnology Information
  (NCBI)
• the field of science in which biology, computer
  science, and information technology merge to form
  a single discipline. The ultimate goal of the
  field is to enable the discovery of new
  biological insights as well as to create a global
  perspective from which unifying principles in
  biology can be discerned.

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What is bioinformatics

• Wikipedia
• Bioinformatics refers to the creation and
  advancement of algorithms, computational and
  statistical techniques, and theory to solve
  formal and practical problems posed by or
  inspired from the management and analysis of
  biological data.

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(No Transcript)
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Course objectives

• Learn the basis of sequence analysis and other
  computational biology algorithms
• Familiarize with the research topics in
  bioinformatics
• Be able to
• Read / criticize bioinformatics research articles
• Identify subareas that best suit your background
• Communicate and exchange ideas with
  (computational) biologists

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What you will learn?

• Basic concepts in molecular biology and genetics
• Algorithms to address selected problems in
  bioinformatics
• Dynamic programming, string algorithms, graph
  algorithms
• Statistical learning algorithms HMM, EM, Gibbs
  sampling
• Data mining clustering / classification
• Applications to real data

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What you will not learn?

• Designing / performing biological experiments
  (duh!)
• Programming (in perl, etc).
• Building bioinformatics software tools (GUI,
  database, Web, )
• Using existing tools / databases (well, not
  exactly true)

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Covered topics
1 week

• Biology
• Sequence analysis
• Sequence alignment
• Pairwise, multiple, global, local, optimal,
  heuristic
• String matching
• Motif finding
• Gene prediction
• RNA structure prediction
• Phylogenetic tree
• Functional Genomics
• Microarray data analysis
• Biological networks

8 weeks
5 weeks
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Computer Scientists vs Biologists(courtesy
Serafim Batzoglou, Stanford)
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Biologists vs computer scientists

• (almost) Everything is true or false in computer
  science
• (almost) Nothing is ever true or false in Biology

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Biologists vs computer scientists

• Biologists seek to understand the complicated,
  messy natural world
• Computer scientists strive to build their own
  clean and organized virtual world

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Biologists vs computer scientists

• Computer scientists are obsessed with being the
  first to invent or prove something
• Biologists are obsessed with being the first to
  discover something

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• Some examples of central role of CS in
  bioinformatics

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1. Genome sequencing
3x109 nucleotides
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1. Genome sequencing
3x109 nucleotides
A big puzzle 60 million pieces
Computational Fragment Assembly Introduced
1980 1995 assemble up to 1,000,000 long DNA
pieces 2000 assemble whole human genome
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2. Gene Finding
Where are the genes?
In humans 22,000 genes 1.5 of human DNA
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2. Gene Finding
Hidden Markov Models (Well studied for many years
in speech recognition)
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3. Protein Folding

• The amino-acid sequence of a protein determines
  the 3D fold
• The 3D fold of a protein determines its function
• Can we predict 3D fold of a protein given its
  amino-acid sequence?
• Holy grail of compbio40 years old problem
• Molecular dynamics, computational geometry,
  machine learning

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4. Sequence ComparisonAlignment
AGGCTATCACCTGACCTCCAGGCCGATGCCC TAGCTATCACGACCGCG
GTCGATTTGCCCGAC
-AGGCTATCACCTGACCTCCAGGCCGA--TGCCC---
x

TAG-CTATCAC--GACCGC--GGTCGATTTGCCCGAC
Sequence Alignment Introduced 1970 BLAST
1990, most cited paper in history Still very
active area of research
BLAST
Efficient string matching algorithms Fast
database index techniques
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Lipman Pearson, 1985
, comparison of a 200-amino-acid sequence to the
500,000 residues in the National Biomedical
Research Foundation library would take less than
2 minutes on a minicomputer, and less than 10
minutes on a microcomputer (IBM PC).
Database size today 1012 (increased by 2 million
folds). BLAST search 1.5 minutes
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5. Microarray analysisClinical prediction of
Leukemia type

• 2 types
• Acute lymphoid (ALL)
• Acute myeloid (AML)
• Different treatments outcomes
• Predict type before treatment?

Bone marrow samples ALL vs AML
Measure amount of each gene
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Some goals of biology for the next 50 years

• List all molecular parts that build an organism
• Genes, proteins, other functional parts
• Understand the function of each part
• Understand how parts interact physically and
  functionally
• Study how function has evolved across all species
• Find genetic defects that cause diseases
• Design drugs rationally
• Sequence the genome of every human, use it for
  personalized medicine
• Bioinformatics is an essential component for all
  the goals above

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• A short introduction to molecular biology

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Life

• Two categories
• Prokaryotes (e.g. bacteria)
• Unicellular
• No nucleus
• Eukaryotes (e.g. fungi, plant, animal)
• Unicellular or multicellular
• Has nucleus

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Prokaryote vs Eukaryote

• Eukaryote has many membrane-bounded compartment
  inside the cell
• Different biological processes occur at different
  cellular location

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Organism, Organ, Cell
Organism
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Chemical contents of cell

• Water
• Macromolecules (polymers) - strings made by
  linking monomers from a specified set (alphabet)
• Protein
• DNA
• RNA
• Small molecules
• Sugar
• Ions (Na, Ka, Ca2, Cl- ,)
• Hormone

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DNA

• DNA forms the genetic material of all living
  organisms
• Can be replicated and passed to descendents
• Contains information to produce proteins
• To computer scientists, DNA is a string made from
  alphabet A, C, G, T
• e.g. ACAGAACGTAGTGCCGTGAGCG
• Each letter is a nucleotide
• Length varies from hundreds to billions

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RNA

• Historically thought to be information carrier
  only
• DNA gt RNA gt Protein
• New roles have been found for them
• To computer scientists, RNA is a string made from
  alphabet A, C, G, U
• e.g. ACAGAACGUAGUGCCGUGAGCG
• Each letter is a nucleotide
• Length varies from tens to thousands

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Protein

• Protein the actual worker for almost all
  processes in the cell
• Enzymes speed up reactions
• Signaling information transduction
• Structural support
• Production of other macromolecules
• Transport
• To computer scientists, protein is a string made
  from 20 kinds of characters
• E.g. MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGP
• Each letter is called an amino acid
• Length varies from tens to thousands

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DNA/RNA zoom-in

• Commonly referred to as Nucleic Acid
• DNA Deoxyribonucleic acid
• RNA Ribonucleic acid
• Found mainly in the nucleus of a cell (hence
  nucleic)
• Contain phosphoric acid as a component (hence
  acid)
• They are made up of a string of nucleotides

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Nucleotides

• A nucleotide has 3 components
• Sugar ring (ribose in RNA, deoxyribose in DNA)
• Phosphoric acid
• Nitrogen base
• Adenine (A)
• Guanine (G)
• Cytosine (C)
• Thymine (T) or Uracil (U)

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Monomers of RNA ribo-nucleotide

• A ribonucleotide has 3 components
• Sugar - Ribose
• Phosphate group
• Nitrogen base
• Adenine (A)
• Guanine (G)
• Cytosine (C)
• Uracil (U)

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Monomers of DNA deoxy-ribo-nucleotide

• A deoxyribonucleotide has 3 components
• Sugar Deoxy-ribose
• Phosphate group
• Nitrogen base
• Adenine (A)
• Guanine (G)
• Cytosine (C)
• Thymine (T)

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Polymerization Nucleotides gt nucleic acids
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5
Free phosphate
5 prime
3 prime
5-AGCGACTG-3
AGCGACTG
DNA
Often recorded from 5 to 3, which is the
direction of many biological processes. e.g. DNA
replication, transcription, etc.
Base
5
Phosphate
Sugar
1
4
2
3
3
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5
Free phosphate
5 prime
3 prime
5-AGUGACUG-3
AGUGACUG
RNA
Often recorded from 5 to 3, which is the
direction of many biological processes. e.g.
translation.
3
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3
5
Base-pair A T G C
Forward () strand
5-AGCGACTG-3 3-TCGCTGAC-5
Backward (-) strand
AGCGACTG TCGCTGAC
One strand is said to be reverse- complementary
to the other
5
3
DNA usually exists in pairs.
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DNA double helix
G-C pair is stronger than A-T pair
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Reverse-complementary sequences

• 5-ACGTTACAGTA-3
• The reverse complement is
• 3-TGCAATGTCAT-5
• gt
• 5-TACTGTAACGT-3
• Or simply written as
• TACTGTAACGT

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Orientation of the double helix

• Double helix is anti-parallel
• 5 end of each strand pairs with 3 end of the
  other
• 5 to 3 motion in one strand is 3 to 5 in the
  other
• Double helix has no orientation
• Biology has no forward and reverse strand
• Relative to any single strand, there is a
  reverse complement or reverse strand
• Information can be encoded by either strand or
  both strands
• 5TTTTACAGGACCATG 3
• 3AAAATGTCCTGGTAC 5

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RNA

• RNAs are normally single-stranded
• Form complex structure by self-base-pairing
• AU, CG
• Can also form RNA-DNA and RNA-RNA double strands.
• AT/U, CG

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Protein zoom-in

• Protein is the actual worker for almost all
  processes in the cell
• A string built from 20 letters
• E.g. MGDVEKGKKIFIMKCSQCHTVEKGGKH
• Each letter is called an amino acid
• R
• H2N--C--COOH
• H

Side chain
Generic chemical form of amino acid
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Amino acid

• 20 amino acids, only differ at side chains
• Each can be expressed by three letters
• Or a single letter A-Y, except B, J, O, U, X, Z
• Alanine Ala A
• Histidine His H

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Amino acids gt peptide
R
R
H2N--C--COOH
H2N--C--COOH

H H
R R

H2N--C--CO--NH--C--COOH

H H

Peptide bond
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Protein

• Has orientations
• Usually recorded from N-terminal to C-terminal
• Peptide vs protein basically the same thing
• Conventions
• Peptide is shorter (lt 50aa), while protein is
  longer
• Peptide refers to the sequence, while protein has
  2D/3D structure

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Protein structure

• Linear sequence of amino acids folds to form a
  complex 3-D structure.
• The structure of a protein is intimately
  connected to its function.

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Genome and chromosome

• Genome the complete DNA sequences in the cell of
  an organism
• May contain one (in most prokaryotes) or more (in
  eukaryotes) chromosomes
• Chromosome a single large DNA molecule in the
  cell
• May be circular or linear
• Contain genes as well as junk DNAs
• Highly packed!

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Formation of chromosome
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Formation of chromosome
50,000 times shorter than extended DNA
The total length of DNA present in one adult
human is the equivalent of nearly 70 round trips
from the earth to the sun
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Gene

• Gene unit of heredity in living organisms
• A segment of DNA with information to make a
  protein

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Some statistics
Chromosomes Bases Genes
Human 46 3 billion 20k-25k
Dog 78 2.4 billion 20k
Corn 20 2.5 billion 50-60k
Yeast 16 20 million 7k
E. coli 1 4 million 4k
Marbled lungfish ? 130 billion ?
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Human genome

• 46 chromosomes 22 pairs X Y
• 1 from mother, 1 from father
• Female X X
• Male X Y

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Human genome

• Every cell contains the same genomic information
• Except sperms and eggs, which only contain half
  of the genome
• Otherwise your children would have 46 46
  chromosomes

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Cell division mitosis

• A cell duplicates its genome and divides into two
  identical cells
• These cells build up different parts of your body

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Cell division meiosis

• A reproductive cell divides into four cells, each
  containing only half of the genomes
• Diploid gt haploid
• Two haploid cells (sperm egg) forms a zygote
• Which will then develop into a multi-cellular
  organism by mitosis

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Central dogma of molecular biology
DNA replication is critical in both mitosis and
meiosis
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DNA Replication

• The process of copying a double-stranded DNA
  molecule
• Semi-conservative
• 5-ACATGATAA-3
• 3-TGTACTATT-5
• ?
• 5-ACATGATAA-3 5-ACATGATAA-3
• 3-TGTACTATT-5 3-TGTACTATT-5

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• Mutation changes in DNA base-pairs
• Proofreading and error-correcting mechanisms
  exist to ensure extremely high fidelity

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Central dogma of molecular biology
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Transcription

• The process that a DNA sequence is copied to
  produce a complementary RNA
• Called message RNA (mRNA) if the RNA carries
  instruction on how to make a protein
• Called non-coding RNA if the RNA does not carry
  instruction on how to make a protein
• Only consider mRNA for now
• Similar to replication, but
• Only one strand is copied

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Transcription
(where genetic information is stored)
DNA-RNA pair AU, CG TA, GC
(for making mRNA)
Coding strand 5-ACGTAGACGTATAGAGCCTAG-3 Tem
plate strand 3-TGCATCTGCATATCTCGGATC-5 mRNA
5-ACGUAGACGUAUAGAGCCUAG-3
Coding strand and mRNA have the same sequence,
except that Ts in DNA are replaced by Us in
mRNA.
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Translation

• The process of making proteins from mRNA
• A gene uniquely encodes a protein
• There are four bases in DNA (A, C, G, T), and
  four in RNA (A, C, G, U), but 20 amino acids in
  protein
• How many nucleotides are required to encode an
  amino acid in order to ensure correct
  translation?
• 41 4
• 42 16
• 43 64
• The actual genetic code used by the cell is a
  triplet.
• Each triplet is called a codon

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The Genetic Code
Third letter
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Translation

• The sequence of codons is translated to a
  sequence of amino acids
• Gene -GCT TGT TTA CGA ATT-
• mRNA -GCU UGU UUA CGA AUU -
• Peptide - Ala - Cys - Leu - Arg - Ile
• Start codon AUG
• Also code Met
• Stop codon UGA, UAA, UAG

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Translation

• Transfer RNA (tRNA) a different type of RNA.
• Freely float in the cell.
• Every amino acid has its own type of tRNA that
  binds to it alone.
• Anti-codon codon binding crucial.

tRNA-Pro
Anti-codon
Nascent peptide
tRNA-Leu
mRNA
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Transcriptional regulation
Transcription factor
RNA Polymerase
Transcription starting site
gene
promoter

• Will talk more in later lectures
• RNA polymerase binds to certain location on
  promoter to initiate transcription
• Transcription factor binds to specific sequences
  on the promoter to regulate the transcription
• Recruit RNA polymerase induce
• Block RNA polymerase repress
• Multiple transcription factors may coordinate

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Splicing
Transcription starting site
gene
promoter
transcription
Pre-mRNA

• Pre-mRNA needs to be edited to form mature mRNA
• Will talk more in later lectures.

intron
intron
Pre-mRNA
exon
exon
3 UTR
exon
5 UTR
Splicing
Mature mRNA (mRNA)
Open reading frame (ORF)
Start codon
Stop codon
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Summary

• DNA a string made from A, C, G, T
• Forms the basis of genes
• Has 5 and 3
• Normally forms double-strand by reverse
  complement
• RNA a string made from A, C, G, U
• mRNA messenger RNA
• tRNA transfer RNA
• Other types of RNA rRNA, miRNA, etc.
• Has 5 and 3
• Normally single-stranded. But can form secondary
  structure
• Protein made from 20 kinds of amino acids
• Actual worker in the cell
• Has N-terminal and C-terminal
• Sequence uniquely determined by its gene via the
  use of codons
• Sequence determines structure, structure
  determines function
• Central dogma DNA transcribes to RNA, RNA
  translates to Protein
• Both steps are regulated

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• Experimental techniques to manipulate DNA

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DNA synthesis

• Creating DNA synthetically in a laboratory
• Chemical synthesis
• Chemical reactions
• Arbitrary sequences
• Maximum length 160-200
• Cloning make copies based on a DNA template
• Biological reactions
• Requires template
• Many copies of a long DNA in a short time

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in vivo DNA Cloning

• Connect a piece of DNA to bacterial DNA, which
  can then be replicated together with the host DNA

bacterial DNA
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in vitro DNA Cloning

• Polymerase chain reaction (PCR)

5
5
denature
5
5
Primer (lt 30 bases)
5
5
5
5
DNA Polymerase
dNTP
5
5
5
5
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Some terms

• Denature a DNA double-strand is separated into
  two strands
• By raising temperature
• Renature the process that two denatured DNA
  strands re-forms a double-strand
• By cooling down slowly
• Hybridization two heterogeneous DNAs form a
  double-stranded DNA
• may have mismatches
• The rationale behind many molecular biological
  techniques including DNA microarray

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DNA sequencing technology

• Read out the letters from a DNA sequence

1974, Frederick Sanger
GTGAGGCGCTGC
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DNA sequencing Basic idea

• PCR
• primer extension
• 5-TTACAGGTCCATACTA ?
• 3-AATGTCCAGGTATGATACATAGG-5
• We need to supply A, C, G, T for the synthesis to
  continue
• Besides A, C, G, T, we add some A, C, G, and
  T
• Very similar to ACGT in all aspects, except that
• The extension will stop if used

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DNA sequencing, cont
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DNA sequencing, cont
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(No Transcript)
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Advances in DNA sequencing

• 1969 three years to sequence 115nt DNA
• 1979 three years to sequence 1650nt
• 1989 one week to sequence 1650nt
• 1995 Haemophilus genome sequenced at TIGR -
  1,830,138nt
• 2000 Human Genome - working draft sequence, 3
  billion bases
• 2003 (near) completion of human genome

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The bioinformatics landmark

• Completion of human genome sequencing is a
  success embraced by
• Advancement in sequencing technology
• Speed of computation
• Algorithm development in bioinformatics
• HGP (Human Genome Project) strategy
• Hierarchical sequencing
• Estimated 15 years (1990 2005), completed in 13
  years
• 3 billion
• Celera strategy
• Whole-genome shotgun sequencing
• Three years (1998-2001)
• 300 million

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Now

• Over 300 genomes have been sequenced
• 1011 - 1012 nt

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2007

• Genomes of three individual human were sequenced
• James Watson
• Craig Venter
• TBN Chinese
• Cost for sequencing Watsons genome
• 3 million, 2 months
• Compared to 3 billion, 13 years for HGP

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• Sequencing speed has been tremendously improved
• High efficiency and relatively low cost makes it
  possible to sequence the genome of any individual
  from any species
• Whats next?

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• Continue to sequence more species?
• More individuals?
• What to do with those sequences?

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• Coming next biological sequence analysis