Annotation Error in Public Databases Misannotation of Molecular Function in Enzyme Superfamilies 英文参考文献.docVIP
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Annotation Error in Public Databases Misannotation of Molecular Function in Enzyme Superfamilies 英文参考文献
AnnotationErrorinPublicDatabases:Misannotationof
MolecularFunctioninEnzymeSuperfamilies
AlexandraM.Schnoes1,ShoshanaD.Brown2,IgorDodevski3,PatriciaC.Babbitt2,4,5*
1Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America, 2Department of Bioengineering and
TherapeuticSciences,UniversityofCaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica,3DepartmentofBiochemistry,UniversityofZu¨rich,Zu¨rich,
Switzerland,4DepartmentofPharmaceuticalChemistry,UniversityofCaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica,5CaliforniaInstitutefor
QuantitativeBiosciences,UniversityofCaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica
Abstract
Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public
databaseshavenotbeenexperimentallycharacterized;rather,sequencesareannotatedusingcomputationalanalysis.The
levelofmisannotationandthetypesofmisannotationinlargepublicdatabasesarecurrentlyunknownandhavenotbeen
analyzedindepth.Wehaveinvestigatedthemisannotationlevelsformolecularfunctioninfourpublicproteinsequence
databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for
which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest
annotationerrorlevels(closeto0%formostfamilies);thetwootherproteinsequencedatabases(GenBankNRandTrEMBL)
andtheproteinsequencesintheKEGGpathwaysdatabaseexhibitsimilarandsurprisinglyhighlevelsofmisannotationthat
average5%–63%acrossthesixsuperfamiliesstudied.For10ofthe37familiesexamined,thelevelofmisannotationinone
ormoreofthesedatabasesis.80%.ExaminationoftheNRdatabaseovertimeshowsthatmisannotationhasincreased
from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with
‘‘overprediction’’ of molecular function. These results suggest that misa
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