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

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2 Dr. Awwad Abdoh Radwan Dept Pharm Organic Chemistry, Faculty of Pharmacy, Assiut University. 29/09/2005

3 Required Texts Image Source:

4 Other Bioinformatics Books Image Source:

5 Other Reference Books Image Source:

6 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

7 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

8 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!

9 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

10 What skills are needed? Well-grounded in one of the following areas: Computer science Molecular biology Statistics Working knowledge and appreciation in the others!

11 Overview of Molecular Biology Cells Chromosomes DNA RNA Amino Acids Proteins Genome/Transcriptome/Proteome CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

Cells Complex system enclosed in a membrane Organisms are unicellular (bacteria, baker s yeast) or multicellular Humans: 60 trillion cells 320 cell types

12 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 Cell biology_intro.htm CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

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

13 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 Karyotype Session8/Session8.html CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

14 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.

15 Nucleotide Bases Purines (A and G) Pyrimidines (C and T) Difference is in base structure Image Source: biology_intro.htm CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

DNA polynucleotides(oligomers) Different nucleotides are strung together to form polynucleotides Ends of the polynucleotide are different A

16 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

17 Single Strand Polynucleotide Example polynucleotide: 5 G T A A A G T C C C G T T A G C 3

18 Double Stranded DNA Source: unknown

19 Double Helix Two complementary DNA strands form a stable DNA double helix Spring 2003 marked the 50 th anniversary of its discovery Image source; biology_intro.htm

20 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

21 mrna Messenger RNA Linear molecule encoding genetic information copied from DNA molecules Transcription: process in which DNA is copied into an RNA molecule

22 mrna Processing Image source:

23 trna structure Source:

24 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

25 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 CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

26 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 20 Amino Acids

27 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

28 Protein Structure Image source:

29 Central Dogma DNA RNA PROTEIN Image source: unknown CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

30 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

31 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: biotechnology_2.html CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

32 History Of Genetic Code Genetic Code Completely uncovered (1965) Marshall Nierenberg

33 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) CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

34 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

35 Shotgun Sequencing Approach Developed 1991 TIGR Craig Venter, Hamilton Smith Break genome into millions of pieces Sequence each piece Reassemble into full genomes CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

36 Whole Genome Shotgun Approach reads generated directly from a wholegenome library assemble the genome all at once

37 Base calling and Assembly Software PHRED and PHRAP Developed (1988) PHRED: Base calling software PHRAP: Assists in assembly of sequenced data CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

38 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) CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

39 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 CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

40 Genomes Fruit Fly Mouse Rat Rice Zebra fish Puffer fish Chicken Dog Frog CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

41 Growth of GenBank 1982: 600,000 Bases 2002: 28.5 Billion Bases Image source:

42 Other Notables Dayhoff ATLAS Database of Proteins (1960s) Sequence Comparison Algorithms 1970, Needleman-Wunch (global alignment) Protein Databank Brookhaven PDB (1973)

43 Other Notables NMR for protein structure identification (1980) IntelliGenetics Founded DNA and Protein sequence analysis (1980)

44 Other Notables Smith-Waterman algorithm Local sequence alignment (1981) GenBank Database created (1982) Genetics Computer Group Founded GCG suite (1982) PCR First Described (1985)

45 Other Notables FASTP Algorithm Protein database searching (1985) SWISS-PROT Protein Database (1986)

46 Other Notables PERL Programming Language Allows for sequence manipulation (1987) NCBI Established (1988) Human Genome Initiative (1988)

47 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) CECS Introduction to Bioinformatics University of Louisville Spring 2004 Dr. Eric Rouchka

48 Other Notables First Commercial Microarray chips produced (1996) Dolly Cloned (1997) Capillary Sequencing machines introduced (1997)

49 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

50 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

Bioinformatics. ONE Introduction to Biology. Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012

Bioinformatics. ONE Introduction to Biology. Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012 Bioinformatics ONE Introduction to Biology Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012 Biology Review DNA RNA Proteins Central Dogma Transcription Translation