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What Is Bioinformatics? What Is Bioinformatics? What Is What is bioinformatics? What is bioinformatics? •the analysis and interpretation of nucleotide and an interdisciplinary field at the interface of the protein sequences and structures computational and life sciences “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. “ National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/ What is bioinformatics? What is bioinformatics? •the analysis and interpretation of nucleotide and •the analysis and interpretation of nucleotide and protein sequences and structures protein sequences and structures • development of algorithms and software to support • development of algorithms and software to support the acquisition … of biomolecular data the acquisition … of biomolecular data •the development of software that enables efficient access and management of biomolecular information 1 The Origins of Computational Biology Bioinformatics stems from parallel revolutions in biology and computing Amino acid sequencing Turing designs a stored At the beginning of World War II (1939‐1944): Sanger sequences insulin. program computer •The shared program computer had not yet been 1950 Edsac: 1st stored Stein, Moore, Spackman: invented, and there were no programming program computer automatic amino acid languages, databases, or computer networks. analyzer •The relationship between genes and proteins, the molecular basis of genes, the structure of DNA and the genetic code were all unknown. Trends in Biochem. Sci, 99 Automatic recording apparatus used in the chromatographic analysis of mixtures of amino acids EDSAC: The first stored‐program computer. Stein, Moore, Spackman, 1958 2 The Origins of Computational Biology Grace Murray Hopper Amino acid sequencing Turing designs a stored finds the first bug Sanger sequences insulin. program computer 1950 Edsac: 1st stored Stein, Moore, Spackman: program computer automatic amino acid analyzer Grace Murray Hopper co‐invents COBOL and finds the first bug Rear Admiral Grace Hopper over‐seeing her team of programmers, Philadelphia Inquirer, 1957 The Origins of Computational Biology Amino acid sequencing Turing designs a stored Sanger sequences insulin. program computer 1950 Edsac: 1st stored Stein, Moore, Spackman: program computer automatic amino acid analyzer Grace Murray Hopper co‐invents COBOL and finds the first bug Grace Murray Hopper Discovery of DNA structure, Watson, Crick, Franklin 3 The Origins of Computational Biology The helical structure of DNA Determination of the Fortran, Basic, LISP James Watson and Francis Crick genetic code 1960 Rosalind Franklin 1970 The Origins of Computational Biology The genetic code The genetic code is a degenerate, non‐overlapping, triplet code. Crick, Barnett, Brenner, and Watts‐Tobin, 1961 Determination of the Fortran, Basic, LISP genetic code 1960 Determination of On going protein sequen‐ the genetic code cing, Dayhoff publishes the Protein Atlas 1970 4 Atlas of Protein Sequence & Structure The Origins of Computational Biology 1965 ‐ 1978 Determination of the Fortran, Basic, LISP genetic code 1960 On going protein sequen‐ cing, Dayhoff publishes the Protein Atlas Arpanet Margaret Dayhoff PhD in Chemistry, 47 Watson Computing Lab Fellow 47 ‐ 48 1970 The ARPAnet is established, The Origins of Computational Biology precursor to the Internet. Determination of the Fortran, Basic, LISP genetic code Packet switching is invented, which supports flexible, multi‐node network 1960 On going protein sequen‐ cing, Dayhoff publishes the Protein Atlas Arpanet Interface Message Processor (IMP) network is constructed, linking 4, and The Protein Data Bank is then 15 nodes established. 1970 5 The Origins of Computational Biology Protein Data Bank (PDB) Growing collection of X‐ray diffraction protein 1970 structure data Sanger‐Coulson sequencing TCP/IP Maxam‐Gilbert sequencing Development of molecular graphics display for Internet 3D visualization SEARCH program supports remote access First royal email Gilbert, Sanger win Nobel USENET newsgroups Prize 1980 Beginnings of molecular evolution The Origins of Computational Biology early mammal 1970 …atgccaggtcccagtga… Sanger‐Coulson sequencing TCP/IP Maxam‐Gilbert sequencing Internet …atgcaaggagtccgagc……atgcgaggtccagtagt… …atgcaaggagtccgagc… …atgcgaggtccagtagt… First royal email Gilbert, Sanger win Nobel human rat mouse USENET newsgroups …atgcaaggagtcggagc… …atgcgaggtccaacagt… …atgggaggtccagtagt… Prize 1980 …atgcaaggagtcgcagagc… …atgcgaggtctcacagtgt… …atgggaggtctcccagtgt… 6 Sequence similarity → structural similarity Sequence similarity → structural similarity Structure? Structure? …vkltpegtr_wgghpldekflske… …vkltpegtr_wgghpldekflske… …vhltpettrgwgghmldekeiske… Estimate protein structure from a related protein with known …vhltpettrgwgghmldekeiske… structure and similar sequence. Estimate protein structure from a related protein with known structure and similar sequence. Sequence similarity → functional similarity The Origins of Computational Biology ? Congress establishes Genbank 1990 ...atgcgaggattctcgaagacagcga… Human Genome Project ...atgcaaggagtc_cgttgacagagc… begins (DOE) Basic local alignment search tool (BLAST) 28 7 The Origins of Computational Biology BLAST Congress establishes Genbank 1990 Human Genome Project Information begins (DOE) superhighway Basic local alignment search World Wide Web, tool (BLAST) NCSA Mosaic ome The internet we know and love The Origins of Computational Biology Al Gore Creates Bill to Fund "Information Congress establishes Superhighway" Genbank 1990 Human Genome Project Information begins (DOE) superhighway Tim Berners‐Lee proposes a design for information sharing that becomes the World Wide Web Basic local alignment search World Wide Web, tool (BLAST) GenBank goes online. NCSA Mosaic The first web browser Pizza Hut goes on line 8 Genbank BLAST National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/ BLAST The Origins of Computational Biology Google H. Influenzae: 1st whole 1995 genome sequence Yeast –1st eukaryote 1998 C. elegans ‐ 1st animal IBM’s Blue Gene architecture for Fly genome 1999 protein modeling A.thaliana – 1st plant 2000 9 Sequence Assembly Shotgun sequencing DNA molecule Limits of gel electrophoresis: ~ 500bp in one “read” To sequence more than 500 bp: shotgun reads Sequence 500bp fragments separately Combine computationally using sequence comparison Sequence assembly contigs Sequence Assembly The Origins of Computational Biology 2001 Wikipedia, Captcha Draft human genome 2002 Mozilla Foundation: open source, W3P ABI Capillary sequencer patent policy 2003 Chimp genome, aligned All-vs-allAlignmentDetermination sequence of sequences of consensus similarity with sequence comparisonhigh sequence with human genome identity 10 How to interpret whole genome How to interpret whole genome sequence sequence •Where are the genes? Where are the genes? •When and where are those genes expressed? •When and where are those genes expressed? •What proteins do they encode? •What proteins do they encode? •What do they do? •What do they do? – Molecular function? – Molecular function? – Biological pathway or process? – Biological pathway or process? atatactcacagcataactgtatatacacccagggggcggaatgaaagcgttaacggcca ggcaacaagaggtgtttgatctcatccgtgatcacatcagccagacaggtatgccgccga cgcgtgcggaaatcgcgcagcgtttggggttccgttccccaaacgcggctgaagaacatc DNA PATTERNS IN THE E.coli lexA GENE tgaaggcgctggcacgcaaaggcgttattgaaattgtttccggcgcatcacgcgggattc gtctgttgcaggaagaggaagaagggttgccgctggtaggtcgtgtggctgccggtgaac Promotor sequences cacttctggcgcaacagcatattgaaggtcattatcaggtcgatccttccttattcaagc Repressor binding site cgaatgctgatttcctgctgcgcgtcagcgggatgtcgatgaaagatatcggcattatgg 1 gaattcgataaatcctggtttattgtgcagtttatggttccaaaatcgccttttgctgt atggtgacttgctggcagtgcataaaactcaggatgtacgtaacggtcaggtcgttgtcg TTCCAA -35 cacgtattgatgacgaagttaccgttaagcgcctgaaaaaacagggcaataaagtcgaac 61 atatactcacagcataactgtatatacacccagggggcggaatgaaagcgttaacggcca tgttgccagaaaatagcgagtttaaaccaattgtcgttgaccttcgtcagcagagcttca -10 TATACT mRNAstart+ +10GGGGG Ribosomal binding site cgcgtgcggaaatcgcgcagcgtttggggttccgttccccaaacgcggctgaagaacatc 121 ggcaacaagaggtgtttgatctcatccgtgatcacatcagccagacaggtatgccgccga tgaaggcgctggcacgcaaaggcgttattgaaattgtttccggcgcatcacgcgggattc 181 cgcgtgcggaaatcgcgcagcgtttggggttccgttccccaaacgcggctgaagaacatc gtctgttgcaggaagaggaagaagggttgccgctggtaggtcgtgtggctgccggtgaac 241 tgaaggcgctggcacgcaaaggcgttattgaaattgtttccggcgcatcacgcgggattc ccattgaagggctggcggttggggttattcgcaacggcgactggctgtaacatatctctg 301 gtctgttgcaggaagaggaagaagggttgccgctggtaggtcgtgtggctgccggtgaac gaattcgataaatctctggtttattgtgcagtttatggttccaaaatcgccttttgctgt 361 cacttctggcgcaacagcatattgaaggtcattatcaggtcgatccttccttattcaagc agaccgcgatgccgcctggcgtcgcggtttgtttttcatctctcttcatcaggcttgtct 421 cgaatgctgatttcctgctgcgcgtcagcgggatgtcgatgaaagatatcggcattatgg ATG…TAA gcatggcattcctcacttcatctgataaagcactctggcatctcgccttacccatgattt 481 atggtgacttgctggcagtgcataaaactcaggatgtacgtaacggtcaggtcgttgtcg open reading frame cgaatgctgatttcctgctgcgcgtcagcgggatgtcgatgaaagatatcggcattatgg 541 cacgtattgatgacgaagttaccgttaagcgcctgaaaaaacagggcaataaagtcgaac atggtgacttgctggcagtgcataaaactcaggatgtacgtaacggtcaggtcgttgtcg 601 tgttgccagaaaatagcgagtttaaaccaattgtcgttgaccttcgtcagcagagcttca cacgtattgatgacgaagttaccgttaagcgcctgaaaaaacagggcaataaagtcgaac 661 ccattgaagggctggcggttggggttattcgcaacggcgactggctgtaacatatctctg tgttgccagaaaatagcgagtttaaaccaattgtcgttgaccttcgtcagcagagcttca 721 agaccgcgatgccgcctggcgtcgcggtttgtttttcatctctcttcatcaggcttgtct
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