Practical Applications of Sequence AnalysisInstructor (Me)Time and PlaceWorld-Wide-Web SiteDiscussion ListEmailSequence analysis at UABCourse ContentGCG Genetics Computer GroupGCG CostsGCG InterfacesOther Useful ProgramsMicrocomputer Sequence Analysis PackagesPros and ConsReference MaterialGCG DocumentationGCG Users GuideGCG Program ManualSeqLab User’s Guide and TutorialSeqWeb InterfaceSequence Analysis TextsA Practical Guide to the Analysis of Genes and ProteinsSequence, Structure, and Databanks : A Practical ApproachSequence Analysis PrimerSequence Analysis in Molecular BiologyPhylogenetic Analysis TextsMolecular SystematicsMacCladePAUP 4.0Molecular EvolutionLecture Schedulehttp://genome.microbio.uab.edu/MIC753/schedule.htmGetting StartedDataSequence PatternsSequence SimilaritiesRNAPhylogenetic AnalysisMicroArray AnalysisGenome AnalysisGetting some real work doneGeneral Lecture OutlineInternet-based ToolsGradingClass ProjectsPreparation of a Web-based Bioinformatic SolutionPossible ProjectsProject 1 GuidelinesAnalysis of a gene familyProject 2 GuidleinesComputers and Communications“Analyze” the Sun UNIX ServerAnalyze AccountsAnalyze Accounts…Change Your Password!Run The Programs!!Required HardwareRequired SoftwareCommunications SoftwareMacintoshPCConnection to analyzeFor more information…Next UpPractical Applications of Sequence AnalysisMIC 753 - The Theory and Application of Sequence AnalysisInstructor (Me)Elliot LefkowitzOffice: BBRB 277APhone: 4-1946E-mail: [email protected] and PlaceApril 3 to June 5 2001no class May 17no class May 29Tuesdays: 3:00 – 4:30Thursdays: 1:00 – 2:30BBRB 170World-Wide-Web Sitehttp://genome.microbio.uab.edu/MIC753General InformationHandoutsLecture NotesDiscussion ListLinksDiscussion ListTalk with ElliotAsk questionsGet answersExpress your frustration[email protected]Talk with ElliotAsk questionsGet answersExpress your frustrationPrivate!Send me your Email Address!!Sequence analysis at UABhttp://genome.microbio.uab.eduMany local sites mentioned in this course have links from this pageCourse ContentTools for Sequence AnalysisGCGNCBIDatabasesOther Web-based toolsSpecialized SoftwarePublicationUnderstanding their useGCGGenetics Computer GroupThe Wisconsin PackageComplete package of programs for sequence analysisNucleic acid and Protein databasesSupporting databasesGCG CostsProgram and database costs are subsidized by:UAB Health Services FoundationUAB AIDS CenterGCG InterfacesCommand lineText based commandsUNIXGraphics displaySeqLabXwindowsWindows environmentSeqWebWeb-based sequence analysisOther Useful ProgramsAvailable for:MacintoshWindows PCsUNIX WorkstationsWeb-based toolsMicrocomputer Sequence Analysis PackagesMacintosh and IBMPros and ConsInitially expensiveDatabases supplied on CD-ROMAvailable on-line from GenbankPackages vary in completenessGenerally easy to useReference MaterialGCG DocumentationWeb-basedhttp://genome.microbio.uab.edu/GCG/GCG10/gcgmanual.htmlUsername: gcgPassword: uabOrder from GCGhttp://www.gcg.com/ordering/orderdocform.htmlUNIX documentationGCG Users GuideGCG Manual Version 10.1Basic guide to UNIXRunning GCG programsProgram descriptionsWorking with dataGenerating graphicsGCG Program ManualComplete Program GuideDescriptionInputOutputParametersAlgorithmsExampleSeqLab User’s Guide and TutorialGCG XWindows InterfaceWindows-like controlmenusdialog boxesmouse controlSeqWeb Interfacehttp://gcg.genome.uab.eduFlat-file versionhttp://gcg.genome.uab.edu:90Relational database versionWeb-based access to GCG programsOnline helpSequence Analysis TextsA Practical Guide to the Analysis of Genes and Proteins Strongly RecommendedEditorsAndreas BaxevanisB.F.Francis OuelletteJohn Wiley & Sons, 1998Sequence, Structure, and Databanks : A Practical ApproachEditorsDes HigginsWillie TaylorOxford Univ Press, 2000Sequence Analysis Primer EditorsMichael GribskovJohn DevereuxGroves Press, 1991Sequence Analysis in Molecular BiologyGunnar von Heijne, EditorAcademic Press, 1987Phylogenetic Analysis TextsMolecular SystematicsDavid M. Hillis and Craig Moritz (eds.)Sinauer Associates, 1990MacCladeAnalysis of Phylogeny and Character EvolutionWayne P. Maddison and David R. MaddisonProgram and ManualSinauer Associates, 1992PAUP 4.0Phylogenetic Analysis Using ParsimonyDavid L. SwoffordProgram and ManualMacPC (DOS)UNIXSinauer Associates, 1998Available later this yearMolecular Evolution Computer Analysis of Protein and Nucleic Acid SequencesMethods in Enzymology, Vol. 183, Doolittle, R.F. (ed.)Academic Press, 1990Lecture ScheduleDate Lecture Topic Tu, April 3 1 Introduction; Communications Th, April 5 2 Using Computers - UNIX Tu, April 10 3 Running GCG Programs; Text and Graphics SeqLab: XWindows interface SeqWeb: Web interface Th, April 12 4 Sequence Databases and other Data SeqStore: GCG Oracle-based data staorage and access Tu, April 17 5 Sequence Editing; Fragment Assembly; Genbank Submission Th, April 19 6 Mapping Tu, April 24 7 Pattern Recognition Th, April 26 8 Protein Analysis Tu, May 1 9 Sequence Comparison Th, May 3 10 Database Searching Tu, May 8 11 Multiple Sequence Analysis Th, May 10 12 Prediction of Functional Motifs; Profile Analysis Tu, May 15 13 RNA Secondary Structure Prediction Th, May 17 No Class Mo May 21 Due Date Project 1 - Web-based Bioinformatic Solutions Tu, May 22 14 Phylogenetic Analysis - Theory and Application Th, May 24 15 Microarray Analysis Tu, May 29 No Class Th May 31 16 Genome Mapping, Sequencing, and Analysis Tu Jun 5 17 Genome Projects - Preparing for the future Mo Jun 11 Due Date Project 2 - Analysis of a gene family http://genome.microbio.uab.edu/MIC753/schedule.htmGetting StartedIntroduction; CommunicationsUsing ComputersUNIXRunning GCG ProgramsTextGraphicsSeqLabSeqWebDataSequence and Other DataSeqStoreGenbank ServicesSequence EditingFragment AssemblyGenbank submissionSequence PatternsMappingPattern RecognitionProtein AnalysisSequence SimilaritiesSequence ComparisonDatabase Searching Multiple