05 protein sequence database lecture

《05 protein sequence database lecture》由会员上传分享，免费在线阅读，更多相关内容在学术论文-天天文库。

1、ComputationalMolecularBiologyBiochem218–BioMedicalInformatics231http://biochem218.stanford.edu/ProteinSequenceDatabasesDougBrutlagProfessorEmeritusBiochemistry&Medicine(bycourtesy)2ndHomework•TranscriptsandsplicevariantsNCBI-EvidenceVieweroFullLengthRefSeqcD

2、NAsoUniGeneESTAssembliesodbESTAssembliesENSEMBLGenesoTranscriptsoSpliceVariantsUCSCGenomeBrowseroRefSeqTractsoHumanESTtracksoSplicedESTtracksoUniGeneTrackProteinSequenceandClassificationDatabases•EvolutionSequenceSimilarityorDistanceClusteredintoproteinSup

3、erfamiliesandFamiliesMultiplesequencealignmentprofilesorHiddenMarkovModelsPhylogenies•FunctionSequencemotifs(consensussequences),PositionsSpecificScoringMatrices(PSSMs),Profiles,HiddenMarkovModels(HMMs)oActivesitesoBindingsitesforligands,substrates,DNAoProtei

4、n-proteininteractionsitesEnzymes,Structures,Receptors,Pores,Signals,Regulators•StructureSecondaryStructureTertiaryFolds–HiddenMarkovModelsClusteredintoproteindomains,superfamiliesandfamiliesQuaternaryComplexes-InteractionDatabasesProteinSequenceDatabases

5、(HistoricalOrder)•NationalBiomedicalResearchFoundation(NBRF)=>ProteinIdentificationResource(PIR)–MargaretDayhoff–AtlasofProteinSequences–Phylogenies,evolution,aminoacidsubstitutionmatrices(PAM)anddiscoveringactivesitesinenzymes–PIRSFEvolutionaryFamily,iProClas

6、sFunctionalsiteanalysisandontologies,iProLinktoliterature–UniProt-UniversalProteinResource•SwissProt(EXPASYsite)–AmosBairoch–Manualcurationandannotation–Highlycross-referenced–Manyusefulanalyticaltools(EXPASYTools)–2D-PAGEandMassSpectrometrydatabases–Prositef

7、unctionalmotifdatabase–UniProt-UniversalProteinResource•TREMBL–TranslationofmRNAs(RefSeq),UniGene,openreadingframes(ORFs)andpredictedgenesfromgenomes–Automaticannotations•EMBL=>EBIProteindatabases–Clusters–Interprolinkedtodomainandmotifdatabases(CATH,PANTHER,

8、PRINTs,PROSITE,pFAM,PIRSF,PRODOM,SCOP,SMART,SUPERFAMILY)–Intron-exonstructureandlinkstoORFs,codingregions–UniProt-UniversalProteinResource•NCBIProteinDatabase–ProteinandnrPROdatabaseSwiss