Real-TimePrimerDesignforDNAChipsUseofprimersinPCRandMicroarraysUseofprimersinPCRandMicroarraysMotivation:SelectprimersfromtargetsequencetwoprimersP(forward)andQ(reverse)forPCR,oneprimerforDNAchip(microarray)UsingwindowsizeW,numberofpossibleprimerswithlengthbetweenmandnwithin1windowis:Technique:ThecomputationalmodelTechnique:quantifyinghybridizationconditionsTechnique:quantifyinghybridizationconditionsTechnique:quantifyinghybridizationconditionsForPCR:Pisforwardprimer,QisreverseprimerIdeally,noannealing,length,GCandtempofPequalsQTheoptimizationis:ForDNAchips(Microarrays):Qdoesn’texist.Nopairannealingtostudy.Only5termsleft.Technique:parallelizeSCPCR(p,q)calculationMeltingtemperatureandCGcontent:Simpleadder+dividerUsepipelining1stone:O(m)Subsequentcost:O(1)AnnealingmatrixComplexityforsequentialalgorithm:ForPCR:NumberofchoicesofP(windowsize=Wp):NumberofchoicesofQ(windowsize=Wq):EachdistanceSCPCR(P,Q):Total:Complexityforparallelalgorithm:ForPCR:DistancemeasureSCPCR(P,Q)=O(1)Total:O(S*T)SimilarbutsimplerforMicroarrayEvaluationRelatedWorkMoreRelatedWorksObservations