外文资料--Monte Carlo Simulations of Spatial Patterns of the Degree of (2).PDF外文资料--Monte Carlo Simulations of Spatial Patterns of the Degree of (2).PDF

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CADVISTVISUALIZATIONTOOLFORBLASTALIGNMENTOFDENGUEVIRUSSEQUENCESBOONYARATVIRIYASAKSATHIAN,YODCHANANWONGSAWATDEPARTMENTOFBIOMEDICALENGINEERING,MAHIDOLUNIVERSITYNAKORNPATHOM,THAILANDG5137363STUDENTMAHIDOLACTHANDEGYWSMAHIDOLACTHPRAPATSURIYAPHOLBIOINFORMATICSANDDATAMANAGEMENTFORRESEARCHUNIT,OFFICEFORRESEARCHANDDEVELOPMENT,FACULTYOFMEDICINESIRIRAJHOSPITAL,MAHIDOLUNIVERSITYBANGKOK,THAILANDSIPURMUCCMAHIDOLACTHABSTRACT–EXPLORATIONOFTHESEARCHENGINETHATCANSIMULTANEOUSLYVISUALIZETHEGENOMICSEQUENCESISONEOFTHECHALLENGINGPROBLEMSINTHISPAPER,WEPROPOSETHESOFTWARE,CALLEDCADVISTTHEUNITXGRAPHICALREPRESENTATIONPREVIOUSLYPROPOSEDBYTHEAUTHORSISEMPLOYEDASTHEALTERNATIVETOOLTOVISUALIZETHERESULTOBTAINEDFROMTHEBASICLOCALALIGNMENTSEARCHTOOLBLASTTHEPROPOSEDSOFTWARECANEFFICIENTLYHELPTHEUSERS/EXPERTSTOEASILYINTERPRETTHERESULTS,ESPECIALLYINDENGUEVIRUSSEQUENCEANALYSISWHEREDIFFERENTSEROTYPESORSUBTYPESNEEDTOBEDISTINGUISHEDKEYWORDSBLAST,DENGUEVIRUS,VISUALIZATION,BIOINFORMATICSIINTRODUCTIONINBIOINFORMATICS,THEBASICLOCALALIGNMENTSEARCHTOOLBLASTISONEOFTHEMOSTWIDELYUSEDTOOLSFORSEQUENCESIMILARITYSEARCHDUETOITSSPEEDANDREASONABLEACCURACYOFSEARCHINGPERFORMANCEHOWEVER,THEBLASTPROGRAMISSTILLLACKEDOFTHEUSERFRIENDLYGRAPHICALREPRESENTATIONHENCE,INTHISPAPER,WEAIMTODEVELOPAVISUALIZATIONTOOLTHATISCAPABLETODISPLAYTHETEXTOUTPUTRESULTINGFROMBLASTTHEREAREMANYEXISTINGTOOLSUSEDFORVISUALIZINGANDANALYZINGTHEGENOMICSEQUENCESEACHTOOLISDEVELOPEDBASEDONSOMESPECIFICTASKSWHICHCANBECATEGORIZEDINTOFOURAPPROACHES,IEBASEVECTOR,SEQUENTIAL,FOURIERTRANSFORMFTANDZCURVEAPPROACHES1BASEVECTORAPPROACHHAMORI,EANDRUSKIN,J1983REPRESENTEDDNASEQUENCESINATHREEDIMENSIONALCURVEHCURVE1GATES,MA1985PROPOSEDTHATGRAPHICALREPRESENTATIONOFDNASEQUENCEINTWODIMENSIONALSPACEWASBETTERTHANHCURVEGATES’GRAPHICALREPRESENTATIONSHOWSFOURNUCLEOTIDEBASES,IEADENINEA,THYMINET,CYTOSINEC,ANDGUANINEGTHEUNITVECTORREPRESENTATIONSOFTHESEBASESAREONTHECARTESIANCOORDINATESYSTEM,IEBASEAISONTHENEGATIVEYAXIS,BASETISONTHEPOSITIVEYAXIS,BASEGISONTHEPOSITIVEXAXIS,ANDBASECISONTHENEGATIVEXAXIS2ABOUTELEVENYEARSLATER,NANDYA1996PROPOSEDAGRAPHICALREPRESENTATIONINORDERTODISTINCTTHEFEATURESOFINTRONANDEXONSEGMENTSOFEUKARYOTICSEQUENCES3THISGRAPHICALREPRESENTATIONWASSIMILARTOGATES’METHODTHEA,G,CANDTNUCLEOTIDEWASPLOTTEDONANACGTAXISSYSTEMTHESLOPEOFTHISPLOTINDICATEDACLUSTEROFINTRONANDEXONSEQUENCESHOWEVER,BOTHNANDYANDGATES’METHODSHAVEHIGHDEGENERACYSUCHTHATTHESEQUENCESSUCHASAGTC,AGTCA,ANDAGTCAGLEADTOTHESAMEGRAPHICALREPRESENTATION4STEPHENS–TYAUETAL,2003MODIFIEDGATES’METHODTHEFOURNUCLEICACIDSARECLASSIFIEDINTOPYRIMIDINE/PURINEGRAPHONTWOQUADRANTSOFTHECARTESIANCOORDINATESYSTEMTHEFIRSTQUADRANTREPRESENTSPYRIMIDINETANDC,ANDTHEFORTHQUADRANTREPRESENTSPURINEAANDG4RECENTLY,THEAUTHORSPROPOSETHEGRAPHICALREPRESENTATIONESPECIALLYFORTHEDENGUEVIRUSSEQUENCEANALYSISBASEDONTHECUMULATIVEAMOUNTOFAMINOANDKETOBASES,CALLEDUNITX52SEQUENTIALAPPROACHALTSCHULETAL,1990DEVELOPEDTHEBASICLOCALALIGNMENTSEARCHTOOLBLASTPROGRAMTHISPROGRAMISONEOFTHEMOSTPOPULARTOOLSFORGENOMICSEQUENCEANALYSISTHISTOOLCANPERFORMAFASTSIMILARITYSEARCHTHEPROGRAMCOMPARESTHESIMILARITYBETWEENANYTWOSEQUENCESANDDISPLAYSTHEDIFFERENCEBETWEENTHESESEQUENCESBYCOMPARINGINTHEBASEBYBASEBASIS63FOURIERTRANSFORMFTAPPROACHANATASSIOUDPROPOSEDTHECOLORSPECTROGRAMSOFBIOMOLECULARSEQUENCESWHICHISTHETOOLUSEDFORVISUALIZATIONOFTHEBIOMOLECULARSEQUENCEANALYSIS7,8SPECTROGRAMSWHICHCANREPRESENTTHEMAGNITUDEOFTHESHORTTIMEFOURIERTRANSFORMSTFTISIMPLEMENTEDVIATHEDISCRETEFOURIERTRANSFORMDFTANALYSISOFTHEGENOMICSEQUENCEINFREQUENCYDOMAINVIATHEFOURIERTRANSFORMFTUSESTHE3PERIODICITYPROPERTYFORDNACODINGSEQUENCETHECOLORSPECTROGRAMISDEFINEDBYUSINGTHECOLORRED,GREENANDBLUEEVENTHOUGHTHISMETHODYIELDSANIMPRESSIVEGRAPHICALREPRESENTATION,THECOMPUTATIONALCOMPLEXITYISFAIRLYHIGH4ZCURVEAPPROACHZHANGCTETAL,1994SUGGESTEDAPRACTICALVISUALIZATIONTOOLCALLEDZCURVE812JAMESJETALDEVELOPEDTHISTOOLINTHEPACKAGECALLEDMBETOOLBOX13ACCORDINGTOTHEASSUMPTIONONTHECUMULATIVECOMPONENTSOFTHEGENOMICSEQUENCE,FEATURESOBTAINEDFROMZCURVECANBEQUICKLYINTERPRETED,SUCHASTHEDISTRIBUTIONALONGTHESEQUENCEOFPURINE/PYRIMIDINEBASES,AMINO/KETOBASES,STRONGHBOND/WEAKHBONDSINCETHEALGORITHMOFZCURVEISSIMPLE,ITCANBEAPPLIEDTOALLGENOMICSEQUENCESREGARDLESSOFHOWLONGTHOSESEQUENCESARETHESIMILARAPPROACHWITHZCURVECALLED3DDCURVEISPRESENTEDBYZHANGYANDTANM2008THISAPPROACHCANBEVIEWEDASTHEWEIGHTEDVERSIONOFZCURVE149781424447138/10/25002010IEEETHECHOICEOFSELECTINGTHEGRAPHICALREPRESENTATIONCANVARYBASEDONTHECHARACTERISTICSOFGENOMICSEQUENCESOFINTERESTTHEREFORE,INTHISFIRSTVERSIONOFTHEPROPOSEDSOFTWARE,DENGUEVIRUSSEQUENCESNEUCLEOTIDESEQUENCESAREEMPLOYEDTOVERIFYTHEMERITOFTHEPROPOSEDSOFTWARETHESOFTWAREISCALLEDCADVISTWHICHSTANDSFORCLASSIFICATIONANDANALYSISOFDENGUEVIRUSSEROTYPEBYVISUALIZATIONTOOLBYEMPLOYINGUNITXASTHEVISULIZATIONTOOL,THEPROPOSEDSOFTWAREISSUITABLETOUSEFORINTEPRETINGTHEDENGUEVIRUSSEQUENCEHOWEVER,POSITIONINGOFPARTIALDENGUESEQUENCESONDENGUEGENOMEWITHUNITXREPRESENTATIONREQUIRESHIGHCOMPUTATIONALLOADBLASTISWELLKNOWNASTHEEFFICIENTSEARCHINGTOOLHOWEVER,VISUALIZINGTHERESULTSOBTAINEDFROMBLASTNEEDSSOMEIMPROVEMENTTHEREFORE,INTHISP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编号:201311201910427491    类型:共享资源    大小:440.40KB    格式:PDF    上传时间:2013-11-20
  
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本文标题:外文资料--Monte Carlo Simulations of Spatial Patterns of the Degree of (2).PDF
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