BIF202 VersionNo.

CoursePrerequisites CourseAntirequisite Objectives: AnalyticalBioinformatics LTPC 3024

ExpectedOutcome:

1.0.1 +2Biology,Mathematics/Introductiontolifesciences,Basic Mathematics Bioinformatics(BIT506) Thiscourseaimsatgivingthestudentbasictechniquesandshow areas of applications in bioinformatics. The aims are more specifically directed to give the student knowledge about common problem in bioinformatics, alignment techniques, ethical issues, public data sources, and evolutionary modelling. The course emphases a practical use of tools for specific bioinformaticareas. 1. Thestudent'sabilitytoapplyhis/herknowledgeof bioinformaticsinapracticalproject. 2. Developtheabilityforcriticalassessmentofscientific researchpublicationsinbioinformatics. 3. Thestudentshouldalsodevelopanunderstandingofthe researchprocessingeneral,suchasresearchmethods, scientificwriting,andresearchethics.

UnitNo.1 Introduction Numberofhours:9 Scope and applications of bioinformatics, Alignment of pairs of sequences; Introduction Definition of sequence alignment, Methods Dot matrix sequence comparisonDynamic programmingalgorithmforsequencealignment. UnitNo.2 Multiplesequencealignment Numberofhours:9 useofmultiplesequencealignmentrelationshipofmultiplesequencealignmenttophylogenetic analysis.Databasesearchingforsimilarsequences.Sequencesimilaritysearch,scoringmatrices forsimilaritysearchesPAMandBlOSUMmatrix. UnitNo.3 Methods Numberofhours:9 FASTAsequencedatabasesimilaritysearch,BLASTsequencedatabasesimilaritysearch,other methodsofcomparingdatabaseofsequencesandpatterns. UnitNo.4 NeuralNetworks Numberofhours:9 The Theory Introduction Priors & likelihoods Learning algorithms: backpropagation Neural Networks: Applications Sequence encoding & output interpretation Sequence correlations&neuralnetworksPredictionofproteinsecondarystructurePredictionofsignal peptides&theircleavagesitesApplicationsforDNA&RNAnucleotidesequences UnitNo.5 HiddenMarkovModels Numberofhours:9 The Theory Introduction Prior information & initialization Likelihood & basic algorithms LearningalgorithmsApplicationsofHMMs:generalaspectsProteinapplicationsDNA&RNA applicationsAdvantages&limitationsofHMMs

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Textbooks

1. Bioinformatics:SequenceandGenomeAnalysisDavidW.Mount, DavidMount 2. Bioinformatics:theMachineLearningApproachPierreBaldiand SrenBrunakPublisher:MITPress. 1. HoomanHRashidi,LukasKBuehler.BioinformaticsBasics. 2000. 2. PerJambeck,CynthiaGibas.DevelopingBioinformaticsComputer Skills.Computers2001. 3. 3.BioinformaticsMethodsandProtocols:MethodsandProtocols. editedbyStephenMisener,StephenAKrawetzScience1999.

ReferenceBooks

S.No. 1. 2. 3. 4. 5. 6. 7. 8. 9.

Experiment SequenceRetrievalSwissprot SequenceRetrievalNCBI PIR AnalysisofPrimaryStructure SequenceanalysisPairwisealignment(PIR) SequenceanalysisFASTA SequenceanalysisBLAST SequenceanalysisMSA ClustalW SequenceanalysisMSA ClustalX Buildingphylogenetictrees

ModeofEvaluation RecommendedbytheBoardofStudies on22ndNov2011

Announced/UnannouncedQuiz/tests, AssignmentsandWrittenExamination Approvedby16th AcademicCouncil

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