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1、BioinfmaticsBioinfmatics?ba?.o???nf?r?mt?ksisabranchofbiologicalsciencewhichdealswiththestudyofmethodsfstingretrievinganalyzingbiologicaldatasuchasnucleicacid(DNARNA)proteinsequencestructurefunctionpathwaysgeicinteractio
2、ns.Itgeneratesnewknowledgethatisusefulinsuchfieldsasdrugdesigndevelopmentofnewsoftwaretoolstocreatethatknowledge.Bioinfmaticsalsodealswithalgithmsdatabasesinfmationsystemswebtechnologiesartificialintelligencesoftcomputin
3、ginfmationcomputationtheystructuralbiologysoftwareengineeringdataminingimageprocessingmodelingsimulationdiscretemathematicscontrolsystemtheycircuittheymonlyusedsoftwaretoolstechnologiesinthisfieldincludeJavaXMLPerlCCPyth
4、onRMySQLSQLCUDAMATLABMicrosoftExcel.IntroductionBuildingontherecognitionoftheimptanceofinfmationtransmissionaccumulationprocessinginbiologicalsystemsin1978PaulienHogewegcoinedthetermed“Bioinfmatics“torefertothestudyofinf
5、mationprocessesinbioticsystems[1].Thisdefinitionplacedbioinfmaticsasfieldparalleltobiophysicsbiochemistry.Examplesofrelevantbiologicalinfmationprocessesstudiedintheearlydaysofbioinfmaticsarethefmationofcomplexsocialinter
6、actionstructuresbysimplebehavialrulestheinfmationaccumulationmaintenanceinmodelsofprebioticevolution.Atthebeginningofthe“genomicrevolution“thetermbioinfmaticswasrediscoveredtorefertothecreationmaintenanceofadatabasetoste
7、biologicalinfmationsuchasnucleotidesequencesaminoacidsequences.Developmentofthistypeofdatabaseinvolvednotonlydesignissuesbutthedevelopmentofcomplexinterfaceswherebyresearcherscouldaccessexistingdataaswellassubmitnewrevis
8、eddata.Indertostudyhownmalcellularactivitiesarealteredindifferentdiseasestatesthebiologicaldatamustbecombinedtofmacomprehensivepictureoftheseactivities.Therefethefieldofbioinfmaticshasevolvedsuchthatthemostpressingtaskno
9、winvolvestheanalysisinterpretationofvarioustypesofdata.Thisincludesnucleotideaminoacidsequencesproteindomainsproteinstructures.[2]Theactualprocessofanalyzinginterpretingdataisreferredtoascomputationalbiology.Imptantsubdi
10、sciplineswithinbioinfmaticscomputationalbiologyinclude:oStructures–ProteinsNucleicacidsLigs(includingmetabolitesdrugs)PeptidesoInteractiondataamongtheaboveentitiesincludingmicroarraydatawksofproteinsmetabolites?DynamicoS
11、ystemsBiologycomesunderthiscategyincludingreactionfluxesvariableconcentrationsofmetabolitesoMultiAgentBasedmodellingapproachescapturingcellulareventssuchassignallingtranionreactiondynamicsAbroadsubcategyunderbioinfmatics
12、isstructuralbioinfmatics.MajresearchareasSequenceanalysisMainarticles:SequencealignmentSequencedatabaseSincethePhageΦX174wassequencedin1977[6]theDNAsequencesofthoussofganismshavebeendecodedstedindatabases.Thissequenceinf
13、mationisanalyzedtodeterminegenesthatencodepolypeptides(proteins)RNAgenesregulatysequencesstructuralmotifsrepetitivesequences.Acomparisonofgeneswithinaspeciesbetweendifferentspeciescanshowsimilaritiesbetweenproteinfunctio
14、nsrelationsbetweenspecies(theuseofmolecularsystematicstoconstructphylogeictrees).WiththegrowingamountofdataitlongagobecameimpracticaltoanalyzeDNAsequencesmanually.TodaycomputerprogramssuchasBLASTareuseddailytosearchseque
15、ncesfrommethan260000ganismscontainingover190billionnucleotides.[7]Theseprogramscancompensatefmutations(exchangeddedbases)intheDNAsequencetoidentifysequencesthatarerelatedbutnotidentical.Avariantofthissequencealignmentisu
16、sedinthesequencingprocessitself.Thesocalledshotgunsequencingtechnique(whichwasusedfexamplebyTheInstitutefGenomicResearchtosequencethefirstbacterialgenomeHaemophilusinfluenzae)[8]doesnotproduceentirechromosomes.Insteaditg
17、eneratesthesequencesofmanythoussofsmallDNAfragments(rangingfrom35to900nucleotideslongdependingonthesequencingtechnology).Theendsofthesefragmentsoverlapwhenalignedproperlybyagenomeassemblyprogramcanbeusedtoreconstructthec
18、ompletegenome.Shotgunsequencingyieldssequencedataquicklybutthetaskofassemblingthefragmentscanbequitecomplicatedflargergenomes.FagenomeaslargeasthehumangenomeitmaytakemanydaysofCPUtimeonlargememymultiprocesscomputerstoass
19、emblethefragmentstheresultingassemblywillusuallycontainnumerousgapsthathavetobefilledinlater.Shotgunsequencingisthemethodofchoicefvirtuallyallgenomessequencedtodaygenomeassemblyalgithmsareacriticalareaofbioinfmaticsresea
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