BioinformaticsSearching Sequence Databases.ppt

《BioinformaticsSearching Sequence Databases.ppt》由会员分享，可在线阅读，更多相关《BioinformaticsSearching Sequence Databases.ppt（17页珍藏版）》请在淘文阁 - 分享文档赚钱的网站上搜索。

1、Bioinformatics:Searching Sequence Databases and the Future of BioinformaticsLaurie PepperMPS ThesisApril 27,2001IntroductionBioinformatics:The science of organizing and analyzing data.Molecular BiologyHuman Genome ProjectDataToolsSearch algorithmsDatabasesBioinformaticsWhy this field is importantAmo

2、unt of dataSearchingBioinformaticsGenomics:DNA and RNAProteomics:Protein structure and functionNeuroinformatics:Brain structure and compositionMolecular BiologyDNA and RNABasesStructureProteinAmino AcidsStructureMolecular BiologyDNA/RNA and proteins can be read as“strings”.Examples:ATCGCC (DNA)UGACU

3、U(RNA)ACGHILMPST(Protein)Molecular BiologyGenes-Why they are importantEvolutionProteins-Gene productsDo the work of lifeWhat we want to do with bioinformaticsAlgorithmsTimeExact matchingFinding ABCD in AABCDABBCCDInexact matchingFinding ABCD in ABBCDDAFBCDMultiple string comparisonComputers and Prog

4、ramsDatabasesSearch toolsSubstitution matricesPairwise sequence comparisonMultiple sequence comparisonDatabasesPrivate vs.PublicPublicDNA/RNAGenBankProteinSwiss-ProtPROSITESearch ProgramsPairwise Sequence AlignmentBLASTFASTAMultiple Sequence AlignmentCLUSTAL WSubstitution MatricesSubstitution Matric

5、esDayhoff/PAMBLOSUM Substitution Matrices:SimplifiedThe higher the score,the better a match is.Example:A-A=3A-B=1A-C=0A-D=-3Match 1:AAAA ABABScore:3+1+3+1=8-Match 2:AAAA ABADScore:3+1+3+(-3)=4The FutureBiologyEthical,Legal and Social ImplicationsHuman Genome ProjectFunctional GenomicsMedicineCompute

6、r ScienceAlgorithmsSearch AlgorithmsSequence Variation AlgorithmsReferencesDNA helix:http:/www.ornl.gov/TechResources/Human_Genome/publicat/primer/fig1.htmlGenBank graph:http:/www.ncbi.nlm.nih.gov/Genbank/genbankstats.html BLOSUM 62 matrix:http:/www.blc.arizona.edu/courses/bioinformatics/blosum.html AcknowledgementsProfessor C.ShilepskyProfessor CollmerMPS majorsMy familyAny Questions?