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外文翻译-- VAMA a versatile web-based tool for variability.PDF

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外文翻译-- VAMA a versatile web-based tool for variability.PDF

VAMAAVERSATILEWEBBASEDTOOLFORVARIABILITYANALYSISINMULTIPLYALIGNEDAMINOACIDSEQUENCESVAMAVARIABILITYANALYSISOFMULTIPLEALIGNMENTSADITIGUPTA,ARIDAMANPANDITANDSOMDATTASINHAMATHEMATICALMODELINGANDCOMPUTATIONALBIOLOGYGROUP,CENTREFORCELLULARANDMOLECULARBIOLOGYCSIRHYDERABAD500007,INDIAEMAILSINHACCMBRESINABSTRACTQUANTIFYINGRESIDUEVARIABILITYATEACHCOLUMNINAMULTIPLESEQUENCEALIGNMENTOFAMINOACIDSHELPSININDICATINGTHEIRSIMILARITIES,ANDISUSEFULTOHIGHLIGHTINFORMATIONABOUTTHESIGNIFICANCESOFEACHPOSITIONFROMTHEPERSPECTIVEOFTHEIRSTRUCTURE,FUNCTION,ANDEVOLUTIONITISBECOMINGINCREASINGLYCLEARTHATTHEGROUPSOFAMINOACIDSTHATALLOWCONSERVEDREPLACEMENTVARYWITHTHEPOSITIONOFTHERESIDUEINTHEPROTEINMOSTMULTIPLEALIGNMENTALGORITHMSCATERTOGENERALUSERSANDHENCEDONOTADDRESSTHISSPECIFICFEATUREATOOLFORSCORINGVARIABILITYINMULTIPLYALIGNEDAMINOACIDSEQUENCES,THATALLOWSDIFFERENTCONSERVATIONGROUPS,ISHIGHLYDESIRABLEVAMAVARIABILITYANALYSISOFMULTIPLEALIGNMENTSISASIMPLEYETVERSATILEPROGRAMTHATCALCULATESANDPLOTSRESIDUEVARIABILITYINAGIVENSETOFALIGNEDSEQUENCESBASEDONKNOWNCONSERVATIONGROUPSSPECIFICFORDIFFERENTFUNCTIONALLYIMPORTANTREGIONSOFAPROTEIN,ANDALSOALLOWSUSERDEFINEDGROUPSFORNEWDISCOVERIESVAMAISAVAILABLEATHTTP//203200217184/VAMA/OVERVIEWHTMLKEYWORDSMULTIPLESEQUENCEALIGNMENT,VARIABILITYANALYSIS,RESIDUECONSERVATIONGROUPSIINTRODUCTIONALIGNMENTOFAMINOACIDSEQUENCESISWIDELYAPPLIEDTOIDENTIFYCONSERVATIONOFRESIDUES1VARIABILITYISAMEASUREOFTHEEXTENTOFVARIATIONOFAMINOACIDSATAPOSITIONINMULTIPLESEQUENCEALIGNMENTFUNCTIONALLYIMPORTANTRESIDUESAREKNOWNTOEXHIBITHIGHERCONSERVATION,ORLOWERVARIABILITYMULTIPLESEQUENCEALIGNMENTMSATOOLSALIGNSEQUENCESBASEDONSOMEPREDETERMINEDCLASSIFICATIONOFAMINOACIDS,DEPENDINGONTHEIRPHYSICOCHEMICALPROPERTIES2RECENTSTUDIESHAVESHOWNTHATTHESAMEGROUPOFAMINOACIDSMAYNOTALWAYSBEUSEFUL,ASSEQUENCECONSERVATIONCLASSIFICATIONSVARYWITHTHESTRUCTUREANDFUNCTIONALOFTHEPROTEINFOREXAMPLE,DIFFERENTCLASSIFICATIONSHAVEBEENSHOWNTOEXISTFORRESIDUESINVOLVEDINLIGANDBINDING3,INPROTEINPROTEININTERACTIONINTERFACES4,INMAINTAININGSTRUCTURE5,ANDINDETERMININGPROTEINFUNCTIONALSPECIFICITY68CLASSIFICATIONBYMIRNYANDSHAKHNOVICHMSWASINTENDEDFORPROTEINSTRUCTURECORES6;WILLIAMSON’SWWASTAILOREDTODEALWITHTRANSPORTERPROTEINS8,WHILEGUHAROYANDCHAKRABARTIGCCLASSIFICATIONWASMEANTFORTHESTUDYOFINTERFACIALAMINOACIDS4THISSUGGESTSTHATDIFFERENTSUBSTITUTIONCLASSIFICATIONSSHOULDBEAPPLIEDINMSABASEDUPONSTRUCTURE/FUNCTIONOFTHEPROTEINSPROGRAMMESAVAILABLEFORSTUDYINGCONSERVATIONORVARIABILITYINMULTIPLEALIGNMENTSBASEDONDIFFERENTSCORINGMETHODSARERATHERCOMPLEX9,ANDNONEOFTHEMCONSIDERALLTHEABOVEMENTIONEDPOSITIONSPECIFICFEATURESINPROTEINS1015ATOOLFORSCORINGVARIABILITYINMULTIPLYALIGNEDAMINOACIDSEQUENCES,THATISSIMPLEBUTADDRESSTHISSPECIFICFEATUREOFALLOWINGDIFFERENTCONSERVATIONGROUPS,ISHIGHLYDESIRABLEWEHAVEDEVELOPEDAWEBBASEDPROGRAMVAMATHATQUANTIFIESTHEVARIABILITYOFTHERESIDUESATEACHALIGNEDPOSITIONINMSAUSINGASIMPLESYMBOLDIVERSITYSCORE16HERE,ALLDIFFERENTAMINOACIDRESIDUESPRESENTINAPARTICULARCOLUMNOFTHEALIGNEDSEQUENCESARECONSIDERED,ANDTHESCORE,V,ISCALCULATEDUSINGTHESUMOFTHEFREQUENCYOFEACHRESIDUEAS1211IINNVN−⎡⎤⎛⎞−⎢⎥⎜⎟⎝⎠⎣⎦−∑1WHERE,NIISTHEFREQUENCYOFEACHRESIDUE,ANDNTHETOTALNUMBEROFRESIDUESATTHISPOSITIONTHESUMISOVERALLTHEDIFFERENTTYPESOFAMINOACIDSPRESENTINTHECOLUMNFORCOMPLETECONSERVATIONOFAMINOACIDSATAPARTICULARCOLUMNINTHEMSAIE,NN,THESCORE,V0,INDICATINGNOVARIABILITY;WHEREAS,FORNOCONSERVATIONORTOTALDIVERSITY,THESCOREISV1SINCE,VVARIESBETWEEN0AND1,ANORMALIZEDSCOREISOBTAINED,WHICHISUSEFULFORCOMPARISONOFDIFFERENTMSASBECAUSEOFTHEGENERICNATUREOFSCORINGINVAMA,WHICHISNOTBASEDONANYSTEREOCHEMICALPROPERTYOFTHEAMINOACIDS,VCANBEUSEDTOCALCULATETHERELATIVEFREQUENCIESOFAMINOACIDSFORANYGIVENCLASSIFICATIONHERE,ALONGWITHTHEBASICSCORINGMETHODOLOGYADOPTEDBYCOMMONLYUSEDMSAPROGRAMMECLUSTAL17,SEVERALOPTIONSAREPROVIDEDFORFUNCTIONSPECIFICCLASSIFICATIONSASMENTIONEDEARLIERTHUS,VAMAPROVIDESTHEUSERWITHFLEXIBILITYTOQUANTIFYVARIABILITYUSINGTHESEDIFFERENTCLASSIFICATIONSASREQUIREDIIFEATURESOFVAMAFIG1SHOWSTHEVAMAINTERFACETHEREARETHREEWAYSINWHICHVARIABILITYANALYSISISDONEINVAMABASIC,GROUPBASEDANDREFERENCESEQUENCEBASEDTHEINPUTFORVAMACANBEMULTIPLEALIGNMENTFILESINCLUSTALANDFASTA9781424447138/10/25002010IEEEFIGURE1VAMAINTERFACEFORMATSTHESEFILESCANBEPASTEDONTOTHEVAMAWORKWINDOW,ORMAYBEUPLOADEDUSINGTHE“BROWSE”BUTTONVAMAALSOADDRESSESTHECOMMONPROBLEMOFEXISTENCEOF“GAPS”INTHEALIGNMENTTHEUSERCANDEFINEAGAPCUTOFFFORINCLUDINGRESIDUEPOSITIONSHAVINGGAPSINTHEALIGNMENTFORCOLUMNS,HAVINGMOREGAPSTHANGAPCUTOFF,VARIABILITYISNOTCALCULATEDANDABLANKSPACEISDISPLAYEDINTHEOUTPUTFORCOLUMNSHAVINGGAPSLESSTHANOREQUALTOTHEDEFINEDGAPCUTOFF,THEVALUEOFNISADJUSTEDBYSUBTRACTINGFROMN,THENUMBEROFGAPSATTHATPOSITIONTHESEPOSITIONSAREINDICATEDBYAINTHEOUTPUTVAMACALCULATESTHEVARIABILITYSCOREFOREACHCOLUMNINTHEALIGNMENTBASEDONTHECONSERVATIONGROUPSCHOSENBYTHEUSER,ANDTHEOUTPUTFILECONSISTSOFTHEFOLLOWINGPARTSITHEVARIABILITYSCOREATEACHALIGNEDPOSITION;IISTATISTICSOFTHEVARIABILITYDATADISPLAYINGTHEMEAN,STANDARDDEVIATIONANDRANGEFORTHESAME;ANDIIITHEPLOTOFVARIABILITYVALUESVERSUSALIGNMENTPOSITIONSTHEDATACANBESAVEDBOTHINTEXTANDEXCELFORMATFORFURTHERANALYSISTHEVARIABILITYANALYSISINVAMACANBEDONEINTHEFOLLOWINGTHREEWAYS–ABASICVARIABILITYANALYSISHEREALLAMINOACIDSARECONSIDEREDTOBEINSEPARATECLASSESHENCE,ITDOESNOTTAKEINTOACCOUNTANYSUBSTITUTIONS,ANDANYNONIDENTITYCONTRIBUTESTOTHEVARIABILITYBGROUPBASEDVARIABILITYANALYSISCONSERVATIVESUBSTITUTIONSCANBEACCOUNTEDFORBYCLASSIFYINGAMINOACIDSACCORDINGTOTHEIRPHYSICOCHEMICALPROPERTIESANDPOSITIONALATTRIBUTESVARIABILITYISASSIGNED0FORAPARTICULARPOSITIONIFTHEAMINOACIDSBELONGTOAGROUPINTHESPECIFICCLASSIFICATIONVAMAPROVIDESTHEFOLLOWINGGROUPBASEDANALYSISOPTIONSIDEFAULTCLASSIFICATIONTHISCLASSIFICATIONISSAMEASTHEONEUSEDINCLUSTAL17AMINOACIDSARECLASSIFIEDINTOSTRONGANDWEAKGROUPSBASEDONTHEPHYSICOCHEMICALPROPERTIESANDTHEGONNETPAM250MATRIX18IIMS,GC,ANDWCLASSIFICATIONSSEVERALDIFFERENTCLASSIFICATIONSAREPROPOSEDDEPENDINGUPONTHEFUNCTIONALCONSTRAINTSAPPLICABLEMSCLASSIFICATIONISAPPLICABLETOPROTEINSTRUCTURECORES6,WCLASSIFICATIONISAPPLICABLETOTRANSPORTERPROTEINS8,ANDGCCLASSIFICATIONISAPPLICABLETOTHEINTERFACEAMINOACIDS4THECLASSIFICATIONSAREDESCRIBEDINTHEUSERGUIDEIIIUSERDEFINEDCLASSIFICATIONVARIOUSOTHERCLASSIFICATIONSCHEMESHAVEBEENPROPOSED7VAMAOFFERSUSERSTHEOPTIONTOUSEANYORTHEIROWNCLASSIFICATIONCREFERENCESEQUENCEBASEDVARIABILITYANALYSISREFERENCESEQUENCEISTHESEQUENCEWITHRESPECTTOWHICHTHERESIDUESARENUMBEREDHEREX0INTHEVARIABILITYPLOTCORRESPONDSTOFIRSTRESIDUEOFTHEREFERENCESEQUENCETHISISUSEFULWHENTHE3DIMENSIONALSTRUCTUREOFTHEREFERENCESEQUENCEISAVAILABLETOHELPANALYZETHERESULTSFORPOSITIONSPECIFICCHANGESINOTHERAMINOACIDSEQUENCESINTHEALIGNMENTTHECALCULATIONISFIRSTDONEBASEDUPONDIFFERENTCLASSIFICATIONS,ANDTHENTHERESIDUESARENUMBEREDACCORDINGTOTHEREFERENCESEQUENCEGIVENBYTHEUSERBYTHISMETHODTHEUSERCANACCESSTHEALIGNMENTAGAINSTTHEREFERENCESEQUENCEANEXAMPLEOFANALYSIS,USINGVAMA,ISSHOWNINFIG2ASETOF25AMINOACIDSEQUENCESREPRESENTINGTHEROSMANNFOLD19WEREEXTRACTEDFROMPROTEINDATABANK20CLUSTALALIGNEDSEQUENCESWEREPASTEDASINPUTTOVAMAWEUSEDMSCLASSIFICATIONTOCALCULATETHEVARIABILITY,ANDCOMPAREDITWITHTHEDEFAULTCLUSTALCLASSIFICATIONFIG2AISTHEVARIABILITYPLOTFORMSANDDEFAULTCLASSIFICATIONS,SHOWINGLOWERSCOREFORMSCLASSIFICATIONTHANTHATOFTHEDEFAULTCLASSIFICATIONINFIG2A,GAPCUTOFFOF0ISUSEDTOCALCULATETHESCORESTHUS,FORPOSITIONSWITH1ORMOREGAPS,VARIABILITYISNOTCALCULATEDROSMANNFOLDBEINGANEXAMPLEOFPROTEINSTRUCTURECORE,THERESULTSWITHMSAREMORERELIABLEFIG2BALSOSHOWSTHATTHEMSCLASSIFICATIONGIVESTHELOWESTSTATISTICSWHENCOMPAREDTOOTHERSHEREWESHOWONLYTHEFIRSTSUBSETOFPOSITIONS92100FORWHICHTHEVARIABILITYSCORESWERECALCULATEDCLEARLY,THEMINIMUMVARIABILITYSCOREGIVENBYMSCLASSIFICATIONADVOCATESTHEAPPLICABILITYOFTHISTOOLIMPORTANTLY,INCASEOFAPROTEINLACKINGWELLDEFINEDFUNCTION,VAMAALLOWSCALCULATIONOFTHEVARIABILITYSCOREUSINGTHEGIVENCLASSIFICATIONSTOIDENTIFYFUNCTIONALLYANDSTRUCTURALLYIMPORTANTRESIDUESBASEDONTHEIRCOMPARATIVESCORETHISFEATURE,WHERESEVERALDIFFERENTCLASSIFICATIONSCANBEUSEDTOCALCULATETHEVARIABILITYINMSA,ISUNIQUETOVAMAFIGURE2ANALYSISOFVAMAOUTPUTFOR25AMINOACIDSEQUENCESOFTHEROSSMANFOLDAVARIABILITYPLOTCOMPARINGMSANDDEFAULTCLASSIFICATIONSCORES,BVARIABILITYVALUESOFRESIDUES92TO100,USINGDIFFERENTCLASSIFICATIONS,ALONGWITHMEANANDSTANDARDDEVIATIONSDVAMAINCLUDESSEVERALUSEFULFEATURESFORTHEUSERTHE“USERGUIDE”EXPLAINSALLFEATURESCLEARLYWITHEXAMPLETHE“RELATEDLINKS”PROVIDESLINKSTOOTHERMSATOOLSEGCLUSTALW,TCOFFEE,CINEMA,ETC,ANDUSEFULWEBSITESSUCHAS,NCBI,PDB,SWISSPROT,ANDKEGGA“SEARCH”BUTTONALLOWSSEARCHWITHINVAMAANDTHEWORLDWIDEWEBIIIDISCUSSIONVAMAISASIMPLE,USERFRIENDLY,YETVERSATILE,TOOLFORCALCULATINGTHEVARIABILITYINMULTIPLYALIGNEDPROTEINSEQUENCESVAMASUPPORTSBOTHBASICANDGROUPBASEDANALYSIS,BYCONSIDERINGTHEPHYSICOCHEMICALPROPERTIESOFAMINOACIDS,ASWELLASTHEIRDIFFERENTIALUSAGEFORDIFFERENTTOPOLOGICALDETERMINANTSINTHEPROTEINITQUANTIFIESVARIABILITYINTHESEQUENCESBASEDONAMINOACIDCLASSIFICATIONGROUPSDEPENDINGONTHEABOVEFACTORSGAPCUTOFFFEATUREACTSASANADDITIONALTOOLTOSCORETHESEQUENCESSTATISTICALANALYSISPERFORMEDONTHEVARIABILITYDATA,LIKEMEAN,STANDARDDEVIATIONANDRANGE,CANALSOBEHELPFULINFURTHERANALYSISVAMAIS,THUS,AUSEFULFUNCTIONSPECIFICVARIABILITYANALYSISTOOLTHATALLOWSACOMPARATIVEANALYSIS–AFEATURELACKINGINOTHERSIMILARTOOLSACKNOWLEDGMENTSSTHANKSDEPARTMENTOFBIOTECHNOLOGY,INDIAFORFINANCIALSUPPORTAGTHANKSTHEINDIANACADEMYOFSCIENCESFORASUMMERFELLOWSHIPTOWORKATTHECCMBAPTHANKSTHECOUNCILOFSCIENTIFICANDINDUSTRIALRESEARCHCSIRFORFELLOWSHIPREFERENCES1TFSMITH,ANDMSWATERMAN,“IDENTIFICATIONOFCOMMONMOLECULARSUBSEQUENCES”JMOLBIOL,VOL147,PP195197,19812DJLIPMAN,SFALTSCHUL,ANDJDKECECIOGLU,“ATOOLFORMULTIPLESEQUENCEALIGNMENT”PROCNATLACADSCIUSA,VOL86,PP44124415,19893TJMAGLIERY,ANDLREGAN,“SEQUENCEVARIATIONINLIGANDBINDINGSITESINPROTEINS”BMCBIOINFORMATICS,VOL6,P240,20054MGUHAROY,ANDPCHAKRABARTI,“CONSERVATIONANDRELATIVEIMPORTANCEOFRESIDUESACROSSPROTEINPROTEININTERFACES”PROCNATLACADSCIUSA,VOL102,PP1544715452,20055OSCHUELERFURMAN,ANDDBAKER,“CONSERVEDRESIDUECLUSTERINGANDPROTEINSTRUCTUREPREDICTION”PROTEINSSTRUCTUREFUNCTIONANDBIOINFORMATICS,VOL52,PP225235,20036LAMIRNY,ANDEISHAKHNOVICH,“EVOLUTIONARYCONSERVATIONOFTHEFOLDINGNUCLEUS”JMOLBIOL,VOL308,PP123129,20017WRTAYLOR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