ApicoAP The First Computational Model for Identifying Apicoplast-Targeted Proteins in Multiple Species of Apicomplexa 英文参考文献.docVIP

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ApicoAP The First Computational Model for Identifying Apicoplast-Targeted Proteins in Multiple Species of Apicomplexa 英文参考文献.doc

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ApicoAP The First Computational Model for Identifying Apicoplast-Targeted Proteins in Multiple Species of Apicomplexa 英文参考文献

ApicoAP:TheFirstComputationalModelforIdentifying Apicoplast-TargetedProteinsinMultipleSpeciesof Apicomplexa GokcenCilingir1,ShiraL.Broschat1,2*,AudreyO.T.Lau2 1School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington, United States of America, 2Department of Veterinary MicrobiologyandPathology,PaulG.AllenSchoolforGlobalAnimalHealth,WashingtonStateUniversity,Pullman,Washington,UnitedStatesofAmerica Abstract Background: Most of the parasites of the phylum Apicomplexa contain a relict prokaryotic-derived plastid called the apicoplast.Thisorganelleisimportantnotonlyforthesurvivaloftheparasite,butitsuniquepropertiesmakeitanideal drug target. The majority of apicoplast-associated proteins are nuclear encoded and targeted post-translationally to the organellarlumenviaabipartitesignalingmechanismthatrequiresanN-terminalsignalandtransitpeptide(TP).Attemptsto defineaconsensusmotifthatuniversallyidentifiesapicoplastTPshavefailed. Methodology/Principal Findings: In this study, we propose a generalized rule-based classification model to identify apicoplast-targeted proteins (ApicoTPs) that use a bipartite signaling mechanism. Given a training set specific to an organism,thismodel,calledApicoAP,incorporatesaprocedurebasedonageneticalgorithmtotailoradiscriminatingrule that exploits the known characteristics of ApicoTPs. Performance of ApicoAP is evaluated for four labeled datasets of Plasmodium falciparum, Plasmodium yoelii, Babesia bovis, and Toxoplasma gondii proteins. ApicoAP improves the classificationaccuracyofthepublisheddatasetforP.falciparumto94%,originally90%usingPlasmoAP. Conclusions/Significance:WepresentaparametricmodelforApicoTPsandaproceduretooptimizethemodelparameters foragiventrainingset.Amajorassetofthismodelisthatitiscustomizabletodifferentparasitegenomes.TheApicoAP predictionsoftwareisavailableat/p/apicoap/and. Citation: Cilingir G,BroschatSL, Lau AOT (2012) ApicoAP: TheFirst Computational Model for Identifying A