CS174 Bioinformatics: Course Information and Introduction to Molecular Biology, Assignments of International Women's Voices

Download CS174 Bioinformatics: Course Information and Introduction to Molecular Biology and more Assignments International Women's Voices in PDF only on Docsity! CS174 Bioinformatics Instructor: Xiaohui Xie University of California, Irvine Today’s Goals • Course information • Challenges in bioinformatics/computational biology • Brief intro to molecular biology • Python tutorial References • Recommended Textbooks: – N.C. Jones and P.A. Pevzner. An Introduction to Bioinformatics Algorithms – R. Durbin, S. Eddy, A. Krogh and G. Mitchison. Biological Sequence Analysis • Course Website: http://www.ics.uci.edu/~xhx/courses/CS174/ where lectures, references and problem sets can be found. Why bioinformatics? 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ATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAAATAAAGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCC TTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATAATGTTTTGTATGATTTATAGTTCATACATGCTTCAACTACTTAATAAATGATTGTATGATA ATGTTTTCAATGTAAGATTACTTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCTTCAACTACTTAATAAAT GATTCATACATGCTTCAACTACTGTAAATAATTAATAAATGATTGTATGATAATGTTTTCAATGTAAGAGATTTCGATTATCCTTATAGTTCATACATGCATAGTTCA TACATGCTTCAACTACTT he human genome is 400,000 longer than the sequence shown here. StochasticDeterministic Histone codeEncapsiluation VirusVirus ModularityClass Regulatory codeMethod GeneData RedundantPrecise GenomeComputer Program Genome as a computer program DOE forms Joint Genome Institute Incorporation of 30,000 J GI Cc genes into human genome map Bee JOnT SPNOME NSTI New five-year plan for the HGP in the U.S. published NCHGR becomes NHGRI gis National Hunan Genome Research instinte E coli genome RIKEN Genomic Sciences Center Japon) established Roundworm (C. elegans) genome sequenced Genoscope (French National Genome Sequencing Center) founded Chinese National Human Genome Centers {in Beijing and Shanghai) established Full-scale human sequencing begins Sequence of first human chromosome (chromosome 22) Draft version of human genome sequence completed President Clinton and Prime Minister Bloir support free access to genome information Executive order bans genetic discrimination in U.S. federal workplace Draft version of human genome sequence published Atal cones ¢ Nature i 10,000 full-length humon cDNAs sequenced ammalian ene ollection Draft version of mouse genome sequence completed and published Draft version of Tat genome sequence completed HGP ends with all goals achieved Draft version of rice genome sequence completed and published to be continued. Four Aspects • Biology – What’s the underlying problem? • Algorithm – How to solve the problem efficiently? • Learning – How to model biology systems and learn from observed data? • Statistics – How to differentiate true phenomena from artifacts? Organism {human) ‘7, TOS gene { ° gene { ™ | eae gene { Each cell Each ae nucleus One specific chromosome sa Ahuman body ¢ontainsan chromosome isonelongDNA double helix. is made up identical pair molecule, and of trillions complement of genes are of cells. chromosomes. functional regions of this DNA. Different Life Forms Share a Common Genetic Framework ©1998 GARLAND PUBLISHING  , Teron rani Genomes • The term genome refers to the complete complement of DNA for a given species • The human genome consists of 46 chromosomes – Male: 22 pairs of autosomes + XY – Female: 22 pairs of autosomes + XX • Every cell (except sex cells and mature red blood cells) contains the complete genome of an organism Human Genome (Male) 22 pairs of autosomes + sex chromosomes (XY) Human Genome (Female) 22 pairs of autosomes + sex chromosomes (XX) RNA • RNA is like DNA except: – backbone is a little different – usually single stranded – the base uracil (U) is used in place of thymine (T) • A strand of RNA can be thought of as a string composed of the four letters: A, C, G, U The Genetic Code 64 combinations: 20 amino acids + stop codon Proteins • Proteins are molecules composed of one or more polypeptides • A polypeptide is a polymer composed of amino acids • Cells build their proteins from 20 different amino acids • A polypeptide can be thought of as a string composed from a 20-character alphabet