protein structure prediction, methods and protocol - david m. webster

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1、MethodsinMolecularBiologyMethodsinMolecularBiologyTMVOLUME143ProteinProteinStructureStructurePredictionPredictionMeMethodsandProtocolsthodsandProtocolsEditedbyEditedbyDavidM.WebsterDavidM.WebsterHUMANAPRESSHUMANAPRESSMultipleSequenceAlignment11MultipleSeque

2、nceAlignmentDesmondG.HigginsandWilliamR.Taylor1.IntroductionThealignmentofproteinsequencesisthemostpowerfulcomputationaltoolavailabletothemolecularbiologist.Whereonesequenceisofunknownstruc-tureandfunction,itsalignmentwithanothersequencethatiswellcharacter-

3、izedinbothstructureandfunctionimmediatelyrevealsthestructureandfunctionofthefirstsequence.Thisidealtransferofinformationis,unfortunately,notalwaysattainedandcanfaileitherbecausethetwosequencesareequallyuncharacterized(althoughtheymightalignquitewell)orbecau

4、sethealignmentistoopoortobetrusted.Boththesesituationscanbehelpediftheanalysisisextendedtoincorporatemoresequences.Intheformercase,theadditionoffurthersequencescanrevealportionsoftheproteinthatareimportantinstructureandfunction(evenifthatstructureorfunction

5、isunknown),whereasinthelatter,therevelationofconservedpatternscanhelpaddconfidenceinthealignment.Inthischapter,wedescribetwomethodsthatcanbeusedtoproducemul-tiplesequencealignments.Botharebasedonthesimpleheuristicthatitisbesttoalignthemostsimilarsequencesfi

6、rstandgraduallycombinethese,inahierarchicmanner,intoamultiplesequencealignment.2.MULTAL2.1.OutlineoftheAlgorithmTheProgramMULTALwasoriginallydevisedtodealwithlargenumbersofproteinsequencesthataretypicallyencounteredintheanalysisoflargefami-lies(suchastheimm

7、unogobulinsorglobins)orinsiftingouttheoftenexten-sivecollectionsofsequencesproducedastheresultofasearchacrosstheFrom:MethodsinMolecularBiology,vol.143:ProteinStructurePrediction:MethodsandProtocolsEditedby:D.Webster©HumanaPressInc.,Totowa,NJ12HigginsandTayl

8、orsequencedatabanks.Theseapplicationsarethemaintopicconsideredinthissection.Thosewhowishtousetheprogramonlyasanalignment/editorforasmallnumberofsequenceswouldbebesttoseekouttheprogramCAMELON