Computational Biology, Part 1 IntroductionCourse IntroductionCourse numbersWhat these courses are aboutI expectYou can expectTextbooks for first half of courseWeb pageClass scheduleInformation flowReview of basic biochemistryStructureDNA properties - base compositionDNA properties - melting temperatureSlide 15DNA structure - restriction mapsRestriction map for circular plasmidSlide 18TranscriptionRNA processingRNA splicingTranslationSlide 23Protein localizationSlide 25Postranslational processingRepresenting and Retrieving SequencesDefinitionRepresentation of SequencesCharacter representation of sequencesRepresenting uncertainty in nucleotide sequencesSlide 32The I.U.B. CodeRepresenting uncertainty in protein sequencesSequence File FormatsSequence file formatsExamples of ASCII sequence file formatsSlide 38Slide 39EntrezEntrez Databases http://www.ncbi.nlm.nih.gov/Entrez DatabasesEntrez essentialsEntrez literature searchingEntrez sequence searchingExample Entrez SessionExample Entrez Session: home of EntrezExample Entrez Session: search OMIM for ‘cystic fibrosis’Example Entrez Session: first hit is CFTRExample Entrez Session: after clicking linksNucleotideExample Entrez Session: after clicking linksProteinExample Entrez Session: Protein sequence from original cDNAExample Entrez Session: change ‘Send to’ to ‘File’Example Entrez Session: LinksPubMedExample Entrez Session: paper in PubMed that is relatedExample Entrez Session: Related ArticlesComputation of related articlesComputation of related articles: words consideredView the MeSH terms: change ‘Display’ to ‘Citation’Computation of related articles: weight of each wordComputation on related articles: Similarity score of two articlesExample Entrez Session: search Nucleotide for cftrExample Entrez Session: 1249 hits related to cftrExample Entrez Session: set limits as title and mRNAExample Entrez Session: 46 hits with limitsExample Entrez Session: further narrow it down to humanBlock Diagram for Entrez Literature SearchingReading for next classComputational Biology, Part 1IntroductionComputational Biology, Part 1IntroductionRobert F. MurphyRobert F. MurphyCopyright Copyright  1996, 2000-2009. 1996, 2000-2009.All rights reserved.All rights reserved.Course IntroductionCourse IntroductionWhat these courses are aboutWhat these courses are aboutWhat I expectWhat I expectWhat you can expectWhat you can expectCourse numbersCourse numbers03-510 = 42-434 undergraduate course03-510 = 42-434 undergraduate course03-710 = 42-734 graduate course03-710 = 42-734 graduate courseDifference is additional research paper for Difference is additional research paper for graduate coursegraduate courseWhat these courses are aboutWhat these courses are aboutoverview of ways in which computers are overview of ways in which computers are used to solve problems in biologyused to solve problems in biologysupervised learning of illustrative or supervised learning of illustrative or frequently-used algorithms and programsfrequently-used algorithms and programssupervised learning of programming supervised learning of programming techniques and algorithms selected from techniques and algorithms selected from these usesthese usesI expectI expectstudents will have basic knowledge of biology and students will have basic knowledge of biology and chemistry (at the level of Modern chemistry (at the level of Modern Biology/Chemistry) and willingness to learn moreBiology/Chemistry) and willingness to learn morestudents have some programming experience and students have some programming experience and willingness to work to improve willingness to work to improve heterogeneous class - I plan to include refreshers heterogeneous class - I plan to include refreshers on each new topicon each new topicstudents will ask questions in class and via emailstudents will ask questions in class and via emailYou can expectYou can expectTwo major course sectionsTwo major course sectionsComputational Molecular Biology (Sequence & Structure Analysis)Computational Molecular Biology (Sequence & Structure Analysis)Computational Cell Biology (Modeling and Image Analysis)Computational Cell Biology (Modeling and Image Analysis)Class sessions: lectures/demonstrationsClass sessions: lectures/demonstrationsRecitations: reviews/quizzes/helpRecitations: reviews/quizzes/helpQuizzes on assigned reading/previous lectures (5% of grade)Quizzes on assigned reading/previous lectures (5% of grade)Homework assignments (50% for 03-510, 40% for 03-710)Homework assignments (50% for 03-510, 40% for 03-710)Midterm Midterm March 5 March 5 (20% of grade)(20% of grade)Final (25% of grade)Final (25% of grade)Research Paper (10% for 03-710)Research Paper (10% for 03-710)Grades determined by weighted average of componentsGrades determined by weighted average of componentsCommunication on class matters via email listCommunication on class matters via email listTextbooks for first half of courseTextbooks for first half of courseFor all studentsFor all studentsRequired textbook: An Introduction to Required textbook: An Introduction to Bioinformatics AlgorithmsBioinformatics AlgorithmsRecommended additional textbookRecommended additional textbookBiological Sequence Analysis: Probabilistic models Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids by Durbin et al. (ISBN: of proteins and nucleic acids by Durbin et al. (ISBN: 0-521-62971-3)0-521-62971-3)Web pageWeb pagehttp://www.cmu.edu/bio/education/courses/03510 http://www.cmu.edu/bio/education/courses/03510 or or 0371003710Lecture Notes (as PowerPoint files)Lecture Notes (as PowerPoint files)Homework Assignments (as PDF files)Homework Assignments (as PDF files)Additional materials as neededAdditional materials as neededClass scheduleClass scheduleTuesdays and ThursdaysTuesdays and Thursdays3:00 to 4:20 lecture3:00 to 4:20 lectureFridaysFridays1:30 to 2:20 recitation1:30 to 2:20 recitationInformation flowInformation flowA major task in computational molecular A major task in computational molecular biology is to “decipher” information biology is to “decipher” information contained in biological sequencescontained in biological sequencesSince the nucleotide sequence of a genome Since the nucleotide sequence of a genome contains all information necessary to contains all information necessary