cecs 694-02 introduction to bioinformatics university of … dr.awad.pdf · cecs 694-02...

CECS 694-02 Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka


Dr. Awwad Abdoh Radwan

Dept Pharm Organic Chemistry,

Faculty of Pharmacy,

Assiut University.

29/09/2005


Required Texts

•

Image Source: http://www.amazon.com/


Other Bioinformatics Books



Other Reference Books



Tentative Schedule of Topics• Overview of molecular biology• Pairwise sequence alignment• Multiple sequence alignment• Sequence Databases• Database searching• Construction of phylogenetic trees• RNA secondary structure prediction Microarray

image analysis• Sequence assembly techniques• Gene Prediction• Protein Folding Prediction


What is Bioinformatics/ Computational Biology?

• Bioinformatics: collection and storage of biological information

• Computational biology: development of algorithms and statistical models to analyze biological data

• Bioinformatics/Computational Biology will be interchanged


Why should I care?• SmartMoney ranks

Bioinformatics as #1 among next HotJobs

• Business Week 50 Masters of Innovation

• Jobs available, exciting research potential

• Important information waiting to be decoded!

http://smartmoney.com/consumer/index.cfm?story=working-june02


Why is bioinformatics hot?• Supply/demand: few people adequately

trained in both biology and computer science

• Genome sequencing, microarrays, etc lead to large amounts of data to be analyzed

• Leads to important discoveries

• Saves time and money


What skills are needed?

• Well-grounded in one of the following areas:– Computer science– Molecular biology– Statistics

• Working knowledge and appreciation in the others!


Overview of Molecular Biology

• Cells• Chromosomes• DNA• RNA• Amino Acids• Proteins• Genome/Transcriptome/Proteome


Cells• Complex system enclosed

in a membrane

• Organisms are unicellular (bacteria, baker’s yeast) or multicellular

• Humans:– 60 trillion cells – 320 cell types

Example Animal Cellwww.ebi.ac.uk/microarray/ biology_intro.htm

http://www.ebi.ac.uk/microarray/biology_intro.htm



Chromosomes• In eukaryotes, nucleus

contains one or several double stranded DNA molecules organized as chromosomes

• Humans: – 22 Pairs of autosomes– 1 pair sex chromosomes

Human Karyotypehttp://avery.rutgers.edu/WSSP/StudentScholars/

Session8/Session8.html


What is DNA?• DNA: Deoxyribonucleic Acid

• Single stranded molecule (oligomer, polynucleotide) chain of nucleotides

• 4 different nucleotides:– Adenosine (A)– Cytosine (C)– Guanine (G)– Thymine (T)


Nucleotide Bases

• Purines (A and G)• Pyrimidines (C and T)• Difference is in base structure

Image Source: www.ebi.ac.uk/microarray/ biology_intro.htm



DNA polynucleotides(oligomers)• Different nucleotides

are strung together to form polynucleotides

• Ends of the polynucleotide are different

• A directionality is present

• Convention is to label the coding strand from 5’ to 3’

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookDNAMOLGEN.html


Single Strand PolynucleotideExample polynucleotide:

5’ G→T→A→A→A→G→T→C→C→C→G→T→T→A→G→C 3’


Double Stranded DNA

Source: unknown


Double Helix• Two complementary DNA strands form a stable DNA

double helix

• Spring 2003 marked the 50th anniversary of its discovery

Image source; www.ebi.ac.uk/microarray/ biology_intro.htm



RNA• Ribonucleic Acid• Important in a variety of ways, including

protein synthesis• Similar to DNA• Thymine (T) is replaced by uracil (U)

• RNA can be:– Single stranded– Double stranded– Hybridized with DNA


mRNA

• Messenger RNA

• Linear molecule encoding genetic information copied from DNA molecules

• Transcription: process in which DNA is copied into an RNA molecule


mRNA Processing

Image source: http://departments.oxy.edu/biology/Stillman/bi221/111300/processing_of_hnrnas.htm

http://departments.oxy.edu/biology/Stillman/bi221/111300/processing_of_hnrnas.htm


tRNA structure

Source: http://www.tulane.edu/~biochem/nolan/lectures/rna/frames/trnabtx2.htm


tRNA• Amino acid attached to each tRNA

• Determined by 3 base anticodon sequence (complementary to mRNA)

• Translation: process in which the nucleotide sequence of the processed mRNA is used in order to join amino acids together into a protein with the help of ribosomes and tRNA


Genetic Code

• 4 possible bases (A, C, G, U)• 3 bases in the codon• 4 * 4 * 4 = 64 possible codon sequences• Start codon: AUG• Stop codons: UAA, UAG, UGA• 61 codons to code for amino acids (AUG as

well)• 20 amino acids – redundancy in genetic code


20 Amino Acids• Glycine (G, GLY)• Alanine (A, ALA)• Valine (V, VAL)• Leucine (L, LEU)• Isoleucine (I, ILE)• Phenylalanine (F, PHE)• Proline (P, PRO)• Serine (S, SER)• Threonine (T, THR)• Cysteine (C, CYS)• Methionine (M, MET)• Tryptophan (W, TRP)• Tyrosine (T, TYR)• Asparagine (N, ASN)• Glutamine (Q, GLN)• Aspartic acid (D, ASP)• Glutamic Acid (E, GLU)• Lysine (K, LYS)• Arginine (R, ARG)• Histidine (H, HIS)• START: AUG• STOP: UAA, UAG, UGA


Proteins• Polypeptides having a three dimensional structure.

• Primary–sequence of amino acids constituting the polypeptide chain

• Secondary–local organization into secondary structures such as α helices and β sheets

• Tertiary –three dimensional arrangements of the amino acids as they react to one another due to the polarity and resulting interactions between their side chains

• Quaternary–number and relative positions of the protein subunits


Protein Structure

Image source: www.ebi.ac.uk/microarray/biology_intro.html


Central Dogma

DNA↓

RNA↓

PROTEIN

Image source: unknown


What is a Gene?

• the physical and functional unit of heredity that carries information from one generation to the next

• DNA sequence necessary for the synthesis of a functional protein or RNA molecule


Brief History of Sequencing• Discovery of Complementary Bases

– Erwin Chargaff, 1950

• Discovery of DNA Double Helix– 1953 – only 50 years ago

– James Watson– Francis Crick– Rosland Franklin

Image: www.simr.org.uk/pages/biotechnology/ biotechnology_2.html

http://www.simr.org.uk/pages/biotechnology/biotechnology_2.html


History Of Genetic Code

• Genetic Code Completely uncovered (1965)– Marshall Nierenberg


Brief History of Sequencing• First Protein Sequence

– ~1955 Bovine Insulin (Fred Sanger)

• First DNA Sequence– ~1965 yeast alanine tRNA (77 bases)

• Development of DNA sequencing– Maxam-Gilbert and Sanger Methods (1977)


Genetic Mapping• Sex-linked genes studied since early 1900s

• Gene mapping takes off in late 1970s– David Botstein (RFLPs 1978)

• 1979: 579 Genes Mapped• 2003 ~30,000 Genes Mapped

– Mapping of Huntington’s Disease (First Diseased Gene)• Triplet Repeat• 1983• Nancy Wexler


Shotgun Sequencing Approach

• Developed 1991 TIGR– Craig Venter, Hamilton Smith

• Break genome into millions of pieces– Sequence each piece– Reassemble into full genomes


Whole Genome Shotgun Approach

• reads generated directly from a whole-genome library

• assemble the genome all at once


Base calling and Assembly Software

• PHRED and PHRAP Developed (1988)– PHRED: Base calling software– PHRAP: Assists in assembly of sequenced

data


Available Assemblers• SEQAID (Peltola et al., 1984)• CAP (Huang, 1992)• PHRAP (Green, 1994)• TIGR Assembler (Sutton et al., 1995)• AMASS (Kim et al., 1999)• CAP3 (Huang and Madan, 1999)• Celera Assembler (Myers et al., 2000)• EULER (Pevzner et al., 2001)• ARACHNE (Batzoglou et al., 2002)


Human Genome Project

• Began in 1990 (US DOE – 15 years)– Identify all genes in human DNA– Determine sequence of human genome– Develop faster sequencing technologies– Develop tools for data analysis


Genomes– Fruit Fly– Mouse– Rat– Rice– Zebra fish– Puffer fish– Chicken– Dog– Frog


Growth of GenBank

• 1982: 600,000 Bases

• 2002: 28.5 Billion Bases

Image source: www.ncbi.nlm.nih.gov


Other Notables

• Dayhoff ATLAS Database of Proteins (1960s)

• Sequence Comparison Algorithms– 1970, Needleman-Wunch (global alignment)

• Protein Databank– Brookhaven PDB (1973)


Other Notables

• NMR for protein structure identification (1980)

• IntelliGenetics Founded– DNA and Protein sequence analysis

(1980)


Other Notables• Smith-Waterman algorithm

– Local sequence alignment (1981)

• GenBank Database created (1982)

• Genetics Computer Group Founded– GCG suite (1982)

• PCR First Described (1985)


Other Notables

• FASTP Algorithm – Protein database searching (1985)

• SWISS-PROT – Protein Database (1986)


Other Notables

• PERL Programming Language– Allows for sequence manipulation (1987)

• NCBI Established (1988)

• Human Genome Initiative (1988)


Other Notables• FASTA Program released (1988)

– DNA and Protein sequence database searches

• BLAST Program released (1990)– Allows for quick database searches

• Informax Founded (1990)

• Human Genome Project Begins (1990)


Other Notables

First Commercial Microarray chips produced (1996)

• Dolly Cloned (1997)

• Capillary Sequencing machines introduced (1997)


Microarrays

• Microarray:– New Technology (less than 10 years old)

• Allows study of thousands of genes at same time

– Study genes under different conditions– Glass slide of DNA molecules

• Molecule: string of bases • uniquely identifies gene or unit to be studied


Microarray Image Analysis• Microarrays detect gene

interactions: 4 colors: – Green: high control– Red: High sample– Yellow: Equal– Black: None

• Problem is to quantify image signals

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