Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology 英文参考文献.docVIP

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Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology 英文参考文献.doc

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Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic Similarities and a Weighting Scheme in Gene Ontology 英文参考文献

RapidAnnotationofAnonymousSequencesfrom GenomeProjectsUsingSemanticSimilaritiesanda WeightingSchemeinGeneOntology PaoloFontana1,AlessandroCestaro1,RiccardoVelasco1,ElideFormentin2,StefanoToppo3* 1FEM-IASMA Research Center, San Michele all’Adige (TN), Italy, 2Department of Biology, University of Padova, Padova, Italy, 3Department of Biological Chemistry, UniversityofPadova,Padova,Italy Abstract Background:Large-scalesequencingprojectshavenowbecomeroutinelabpracticeandthishasledtothedevelopment ofanewgenerationoftoolsinvolvingfunctionpredictionmethods,bringingthelatterbacktothefore.TheadventofGene Ontology,withitsstructuredvocabularyandparadigm,hasprovidedcomputationalbiologistswithanappropriatemeans forthistask. Methodology:WepresenthereanovelmethodcalledARGOT(AnnotationRetrievalofGeneOntologyTerms)thatisableto processquicklythousandsofsequencesforfunctionalinference.Thetoolexploitsforthefirsttimeanintegratedapproach which combines clustering of GO terms, based on their semantic similarities, with a weighting scheme which assesses retrieved hits sharing a certain number of biological features with the sequence to be annotated. These hits may be obtainedbydifferentmethodsandinthisworkwehavebasedARGOTprocessingonBLASTresults. Conclusions:Theextensivebenchmarkinvolved10,000proteinsequences,thecompleteS.cerevisiaegenomeandasmall subsetofproteinsforpurposesofcomparisonwithotheravailabletools.Thealgorithmwasproventooutperformexisting methodsandtobesuitableforfunctionpredictionofsingleproteinsduetoitshighdegreeofsensitivity,specificityand coverage. Citation: Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S (2009) Rapid Annotation of Anonymous Sequences from Genome Projects Using Semantic SimilaritiesandaWeightingSchemeinGeneOntology.PLoSONE4(2):e4619.doi:10.1371/journal.pone.0004619 Editor:SridharHannenhalli,UniversityofPennsylvaniaSchoolofMedicine,UnitedStatesofAmerica ReceivedNovember9,2008;AcceptedJanuary9,2009;PublishedFebruary27,2009 Copyright: ? 2009 Fontana et