EB3233 Bioinformatics Introduction to Bioinformatics

What is Bioinformatics? Bioinformatics is an interdisciplinary research area at the interface between computer science and biological science. Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. Bioinformatics involves the technology that uses computers for storage, retrieval, manipulation, and distribution of information related to biological macromolecules such as DNA, RNA, and proteins. Interface of biology and computers which analysis proteins, genes and genomes using computer algorithms and computer databases

Computational approaches to biological questions Understanding one genome Understanding many genomes Identifying causal genes for a disease Predicting outcome under perturbations String and graph based algorithms for sequence assembly Comparing multiple genomes using trees and hidden markov models Clustering/Network inference Classification/Regression Biological question Computational approach

What is biological data? Information about the elements that make up a living system DNA, RNA, proteins, metabolites interactions among elements Biological data comes in many forms sequence secondary and tertiary structures Knowledge bases: functions activity levels: mRNA, protein, metabolite levels networks of interactions among biomolecules

Biological data: Collection of “omes” Genome: Full DNA sequence complement of an organism Transcriptome: The full RNA complement of an organism (condition-specific) Proteome: The set of all proteins Metabolome: The set of all metabolites Interactome: The set of interactions (protein-protein, protein- DNA, genetic..) …

Biological data comes in many forms Sequence DNA and protein sequence Structure RNA Secondary structure, protein secondary and tertiary structure Real-value measurements Gene expression, protein level Graphs Biological networks

Three perspectives on bioinformatics The cell The organism The tree of life

First perspective: the cell

DNARNAprotein Central dogma of molecular biology genometranscriptomeproteome Central dogma of bioinformatics and genomics

DNARNA cDNA ESTs UniGene phenotype genomic DNA databases protein sequence databases protein Fig. 2.2 Page 18

Growth of GenBank Year Base pairs of DNA (millions) Sequences (millions) Fig. 2.1 Page 17

GenBankEMBLDDBJ Housed at EBI European Bioinformatics Institute There are three major public DNA databases Housed at NCBI National Center for Biotechnology Information Housed in Japan

Time of development Body region, physiology, pharmacology, pathology Second perspective: the organism

After Pace NR (1997) Science 276:734 Third perspective: the tree of life

Overview of lecture topics Assembling genomes Comparing genomes Annotating genomes Analyzing functional genomics datasets (mRNA levels, protein levels) Inferring and analyzing biological networks

Sequencing and assembly: What is the DNA sequence of a organism?

Topics in sequence assembly DNA sequencing Graph theory Shortest substring problem Hamiltonian Paths Survey of popular algorithms in assembly

Sequence comparison: How similar are the sequences?

Topics in sequence alignment Pairwise-alignment Dynamic programming Local and global alignment Algorithms for sequence alignment

How are these organisms related? Tohet al, Nature, 2011

Topics in comparing many genomes Multiple sequence alignment Phylogenetic trees distance-based approaches parsimony-based approaches probabilistic methods examining genetic variation

CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAACACAG CCCTAATCTAACCCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATAC CACTCCGAACCACCATCCATCCCTCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATCCAACCCACTGCCACTT ACCCTACCATTACCCTACCATCCACCATGACCTACTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGT AAATAACACACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTTTACGTACG CACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTCCACTTCACTCCATGGCCCATCTCTCACTGAATCA GTACCAAATGCACTCACATCATTATGCACGGCACTTGCCTCAGCGGTCTATACCCTGTGCCATTTACCCATAACGCCCATCATTAT CCACATTTTGATATCTATATCTCATTCGGCGGTCCCAAATATTGTATAACTGCCCTTAATACATACGTTATACCACTTTTGCACCATA TACTTACCACTCCATTTATATACACTTATGTCAATATTACAGAAAAATCCCCACAAAAATCACCTAAACATAAAAATATTCTACTTTTC AACAATAATACATAAACATATTGGCTTGTGGTAGCAACACTATCATGGTATCACTAACGTAAAAGTTCCTCAATATTGCAATTTGCT TGAACGGATGCTATTTCAGAATATTTCGTACTTACACAGGCCATACATTAGAATAATATGTCACATCACTGTCGTAACACTCTTTAT TCACCGAGCAATAATACGGTAGTGGCTCAAACTCATGCGGGTGCTATGATACAATTATATCTTATTTCCATTCCCATATGCTAACC GCAATATCCTAAAAGCATAACTGATGCATCTTTAATCTTGTATGTGACACTACTCATACGAAGGGACTATATCTAGTCAAGACGATA CTGTGATAGGTACGTTATTTAATAGGATCTATAACGAAATGTCAAATAATTTTACGGTAATATAACTTATCAGCGGCGTATACTAAA ACGGACGTTACGATATTGTCTCACTTCATCTTACCACCCTCTATCTTATTGCTGATAGAACACTAACCCCTCAGCTTTATTTCTAGT TACAGTTACACAAAAAACTATGCCAACCCAGAAATCTTGATATTTTACGTGTCAAAAAATGAGGGTCTCTAAATGAGAGTTTGGTAC CATGACTTGTAACTCGCACTGCCCTGATCTGCAATCTTGTTCTTAGAAGTGACGCATATTCTATACGGCCCGACGCGACGCGCCA AAAAATGAAAAACGAAGCAGCGACTCATTTTTATTTAAGGACAAAGGTTGCGAAGCCGCACATTTCCAATTTCATTGTTGTTTATTG GACATACACTGTTAGCTTTATTACCGTCCACGTTTTTTCTACAATAGTGTAGAAGTTTCTTTCTTATGTTCATCGTATTCATAAAATG CTTCACGAACACCGTCATTGATCAAATAGGTCTATAATATTAATATACATTTATATAATCTACGGTATTTATATCATCAAAAAAAAGT AGTTTTTTTATTTTATTTTGTTCGTTAATTTTCAATTTCTATGGAAACCCGTTCGTAAAATTGGCGTTTGTCTCTAGTTTGCGATAGTG TAGATACCGTCCTTGGATAGAGCACTGGAGATGGCTGGCTTTAATCTGCTGGAGTACCATGGAACACCGGTGATCATTCTGGTCA CTTGGTCTGGAGCAATACCGGTCAACATGGTGGTGAAGTCACCGTAGTTGAAAACGGCTTCAGCAACTTCGACTGGGTAGGTTTC AGTTGGGTGGGCGGCTTGGAACATGTAGTATTGGGCTAAGTGAGCTCTGATATCAGAGACGTAGACACCCAATTCCACCAAGTTG ACTCTTTCGTCAGATTGAGCTAGAGTGGTGGTTGCAGAAGCAGTAGCAGCGATGGCAGCGACACCAGCGGCGATTGAAGTTAAT TTGACCATTGTATTTGTTTTGTTTGTTAGTGCTGATATAAGCTTAACAGGAAAGGAAAGAATAAAGACATATTCTCAAAGGCATATA GTTGAAGCAGCTCTATTTATACCCATTCCCTCATGGGTTGTTGCTATTTAAACGATCGCTGACTGGCACCAGTTCCTCATCAAATAT TCTCTATATCTCATCTTTCACACAATCTCATTATCTCTATGGAGATGCTCTTGTTTCTGAACGAATCATAAATCTTTCATAGGTTTCG TATGTGGAGTACTGTTTTATGGCGCTTATGTGTATTCGTATGCGCAGAATGTGGGAATGCCAATTATAGGGGTGCCGAGGTGCCT TATAAAACCCTTTTCTGTGCCTGTGACATTTCCTTTTTCGGTCAAAAAGAATATCCGAATTTTAGATTTGGACCCTCGTACAGAAGC TTATTGTCTAAGCCTGAATTCAGTCTGCTTTAAACGGCTTCCGCGGAGGAAATATTTCCATCTCTTGAATTCGTACAACATTAAACG TGTGTTGGGAGTCGTATACTGTTAGGGTCTGTAAACTTGTGAACTCTCGGCAAATGCCTTGGTGCAATTACGTAATTTTAGCCGCT GAGAAGCGGATGGTAATGAGACAAGTTGATATCAAACAGATACATATTTAAAAGAGGGTACCGCTAATTTAGCAGGGCAGTATTAT TGTAGTTTGATATGTACGGCTAACTGAACCTAAGTAGGGATATGAGAGTAAGAACGTTCGGCTACTCTTCTTTCTAAGTGGGATTT TTCTTAATCCTTGGATTCTTAAAAGGTTATTAAAGTTCCGCACAAAGAACGCTTGGAAATCGCATTCATCAAAGAACAACTCTTCGT TTTCCAAACAATCTTCCCGAAAAAGTAGCCGTTCATTTCCCTTCCGATTTCATTCCTAGACTGCCAAATTTTTCTTGCTCATTTATAA TGATTGATAAGAATTGTATTTGTGTCCCATTCTCGTAGATAAAATTCTTGGATGTTAAAAAATTAAAGGGACTATATCTAGTCAAGAC GATACTGTCAGTAGCAGCGATGGCAGCGTGGCTTGTGGTAGCAACACTATCATGGT Where are the genes in this genome?

CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACACATCCTAACACTACCCTAACACAGCCCTAATCTAAC CCTGGCCAACCTGTCTCTCAACTTACCCTCCATTACCCTGCCTCCACTCGTTACCCTGTCCCATTCAACCATACCACTCCGAACCACCATCCATCCC TCTACTTACTACCACTCACCCACCGTTACCCTCCAATTACCCATATCCAACCCACTGCCACTTACCCTACCATTACCCTACCATCCACCATGACCTA CTCACCATACTGTTCTTCTACCCACCATATTGAAACGCTAACAAATGATCGTAAATAACACACACGTGCTTACCCTACCACTTTATACCACCACCA CATGCCATACTCACCCTCACTTGTATACTGATTTTACGTACGCACACGGATGCTACAGTATATACCATCTCAAACTTACCCTACTCTCAGATTCCA CTTCACTCCATGGCCCATCTCTCACTGAATCAGTACCAAATGCACTCACATCATTATGCACGGCACTTGCCTCAGCGGTCTATACCCTGTGCCAT TTACCCATAACGCCCATCATTATCCACATTTTGATATCTATATCTCATTCGGCGGTCCCAAATATTGTATAACTGCCCTTAATACATACGTTATACCAC TTTTGCACCATATACTTACCACTCCATTTATATACACTTATGTCAATATTACAGAAAAATCCCCACAAAAATCACCTAAACATAAAAATATTCTACTTTTC AACAATAATACATAAACATATTGGCTTGTGGTAGCAACACTATCATGGTATCACTAACGTAAAAGTTCCTCAATATTGCAATTTGCTTGAACGGATGCT ATTTCAGAATATTTCGTACTTACACAGGCCATACATTAGAATAATATGTCACATCACTGTCGTAACACTCTTTATTCACCGAGCAATAATACGGTAGTG GCTCAAACTCATGCGGGTGCTATGATACAATTATATCTTATTTCCATTCCCATATGCTAACCGCAATATCCTAAAAGCATAACTGATGCATCTTTAATC TTGTATGTGACACTACTCATACGAAGGGACTATATCTAGTCAAGACGATACTGTGATAGGTACGTTATTTAATAGGATCTATAACGAAATGTCAAATAA TTTTACGGTAATATAACTTATCAGCGGCGTATACTAAAACGGACGTTACGATATTGTCTCACTTCATCTTACCACCCTCTATCTTATTGCTGATAGAAC ACTAACCCCTCAGCTTTATTTCTAGTTACAGTTACACAAAAAACTATGCCAACCCAGAAATCTTGATATTTTACGTGTCAAAAAATGAGGGTCTCTAAA TGAGAGTTTGGTACCATGACTTGTAACTCGCACTGCCCTGATCTGCAATCTTGTTCTTAGAAGTGACGCATATTCTATACGGCCCGACGCGACGCGC CAAAAAATGAAAAACGAAGCAGCGACTCATTTTTATTTAAGGACAAAGGTTGCGAAGCCGCACATTTCCAATTTCATTGTTGTTTATTGGACATACACT GTTAGCTTTATTACCGTCCACGTTTTTTCTACAATAGTGTAGAAGTTTCTTTCTTATGTTCATCGTATTCATAAAATGCTTCACGAACACCGTCATTGAT CAAATAGGTCTATAATATTAATATACATTTATATAATCTACGGTATTTATATCATCAAAAAAAAGTAGTTTTTTTATTTTATTTTGTTCGTTAATTTTCAATT TCTATGGAAACCCGTTCGTAAAATTGGCGTTTGTCTCTAGTTTGCGATAGTGTAGATACCGTCCTTGGATAGAGCACTGGAGATGGCTGGCTTTAAT CTGCTGGAGTACCATGGAACACCGGTGATCATTCTGGTCACTTGGTCTGGAGCAATACCGGTCAACATGGTGGTGAAGTCACCGTAGTTGAAAACG GCTTCAGCAACTTCGACTGGGTAGGTTTCAGTTGGGTGGGCGGCTTGGAACATGTAGTATTGGGCTAAGTGAGCTCTGATATCAGAGACGTAGACA CCCAATTCCACCAAGTTGACTCTTTCGTCAGATTGAGCTAGAGTGGTGGTTGCAGAAGCAGTAGCAGCGATGGCAGCGACACCAGCGGCGATTGAA GTTAATTTGACCATTGTATTTGTTTTGTTTGTTAGTGCTGATATAAGCTTAACAGGAAAGGAAAGAATAAAGACATATTCTCAAAGGCATATAGTTGAA GCAGCTCTATTTATACCCATTCCCTCATGGGTTGTTGCTATTTAAACGATCGCTGACTGGCACCAGTTCCTCATCAAATATTCTCTATATCTCATCTTT CACACAATCTCATTATCTCTATGGAGATGCTCTTGTTTCTGAACGAATCATAAATCTTTCATAGGTTTCGTATGTGGAGTACTGTTTTATGGCGCTTAT GTGTATTCGTATGCGCAGAATGTGGGAATGCCAATTATAGGGGTGCCGAGGTGCCTTATAAAACCCTTTTCTGTGCCTGTGACATTTCCTTTTTCGG TCAAAAAGAATATCCGAATTTTAGATTTGGACCCTCGTACAGAAGCTTATTGTCTAAGCCTGAATTCAGTCTGCTTTAAACGGCTTCCGCGGAGGAAA TATTTCCATCTCTTGAATTCGTACAACATTAAACGTGTGTTGGGAGTCGTATACTGTTAGGGTCTGTAAACTTGTGAACTCTCGGCAAATGCCTTGGT GCAATTACGTAATTTTAGCCGCTGAGAAGCGGATGGTAATGAGACAAGTTGATATCAAACAGATACATATTTAAAAGAGGGTACCGCTAATTTAGCAG GGCAGTATTATTGTAGTTTGATATGTACGGCTAACTGAACCTAAGTAGGGATATGAGAGTAAGAACGTTCGGCTACTCTTCTTTCTAAGTGGGATTTT TCTTAATCCTTGGATTCTTAAAAGGTTATTAAAGTTCCGCACAAAGAACGCTTGGAAATCGCATTCATCAAAGAACAACTCTTCGTTTTCCAAACAATC TTCCCGAAAAAGTAGCCGTTCATTTCCCTTCCGATTTCATTCCTAGACTGCCAAATTTTTCTTGCTCATTTATAATGATTGATAAGAATTGTATTTGTGT CCCATTCTCGTAGATAAAATTCTTGGATGTTAAAAAATTAAAGGGACTATATCTAGTCAAGACGATACTGTCAGTAGCAGCGATGGCAGCGTGGCTT GTGGTAGCAACACTATCATGGTATCACTAACGTAAAAGTTCCTCAATATTGCAATTTGCTTGAACGGATGCTATTTCAGAATATTTCGTACTTACACAG GCCATACATTAGAATAATATGTCACATCACTGTCGTAACACTCTTTATTCACCGAGCAATAATACGGTAGTGGCTCAAACTCATGCGGGTGCTATGAT ACAATTATATCTTATTTCCATTCCCATATGCTAACCGCAATATCCTAAAAGCATAACTGATGCATCTTTAATCTTGTATGTGACACTACTCATACGA AGGGACTATATCTAGTCAAGACGATACTGTGATAGGTACGTTATTTAATAGGATCTATAACGAAATGTCAAATAATTTTACGGTAATATAACTTAT CAGCGGCGTATACTAAAACGGACGTTACGATATTGTCTCACTTCATCTTACCACCCTCTATCTTATTGCTGATAGAACACTAACCCCTCAGCTTTA TTTCTAGTTACAGTTACACAAAAAACTATGCCAACCCAGAAATCTTGATATTTTACGTGTCAAAAAATGAGGGTCTCTAAATGAGAGTTTGGTACC ATGACTTGTAACTCGCACTGCCCTGATCTGCAATCTTGTTCTTAGAAGTGACGCATATTCTATACGGCCCGACGCGACGCGCCAAAAAATGAAAAAC GAAGCAGCGACTCATTTTTATTTAAGGACAAAGGTTGCGAAGCCGCACATTTCCAATTTCATTGTTGTTTATTGGACATACACTGTTAGCTTTATTACC GTCCACGTTTTTTCTAGCACCATATACTTACCACTCCATTTATGAATCAGTACC Protein coding sequence Regulatory sites

Sequence annotation: What are the genes, and regulatory regions? Genes Chromosome IV

Topics in sequence annotation Markov chains hidden Markov models Forward/Backward/Viterbi algorithms applications to gene finding and motif modeling

What genes are associated with what functions? Measure mRNA/proteins levels under different environmental conditions Compare levels of genes under different conditions Genes Environmental Conditions Gaschet al., 2000

Topics in Data Analysis from High-Throughput Experiments clustering algorithms hierarchical clustering k-means clustering EM-based clustering classification algorithms (simple methods for supervised learning) multiple hypothesis testing and the false discovery rate

What’s next? Introduction to Biological Databases