Not All Sequence Tags Are Created Equal Designing and Validating Sequence Identification Tags Robust to Indels 英文参考文献.docVIP
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Not All Sequence Tags Are Created Equal Designing and Validating Sequence Identification Tags Robust to Indels 英文参考文献
NotAllSequenceTagsAreCreatedEqual:Designingand
ValidatingSequenceIdentificationTagsRobusttoIndels
BrantC.Faircloth1*,TravisC.Glenn2
1DepartmentofEcologyandEvolutionaryBiology,UniversityofCaliforniaLosAngeles,LosAngeles,California,UnitedStatesofAmerica,2DepartmentofEnvironmental
HealthScience,UniversityofGeorgia,Athens,Georgia,UnitedStatesofAmerica
Abstract
Ligatingadapterswithuniquesyntheticoligonucleotide sequences(sequencetags)ontoindividualDNAsamplesbefore
massivelyparallelsequencingisapopularandefficientwaytoobtainsequencedatafrommanyindividualsamples.Tag
sequencesshouldbenumerousandsufficientlydifferenttoensuresequencing,replication,andoligonucleotidesynthesis
errors do not cause tags to be unrecoverable or confused. However, many design approaches only protect against
substitutionerrorsduringsequencingandextanttagsetscontaintoofewtagsequences.Wedevelopedanopen-source
softwarepackagetovalidatesequencetagsforconformancetotwodistancemetricsanddesignsequencetagsrobustto
indelandsubstitutionerrors.Weusethissoftwarepackagetoevaluateseveralcommercialandnon-commercialsequence
tagsets,designseverallargesets(maxcount=7,198)ofeditmetricsequencetagshavingdifferentlengthsanddegreesof
errorcorrection,andintegrateasubsetoftheseeditmetrictagstopolymerasechainreaction(PCR)primersandsequencing
adapters.WevalidateasubsetoftheseeditmetrictaggedPCRprimersandsequencingadaptersbysequencingonseveral
platformsandsubsequentcomparisontocommerciallyavailablealternatives.Wefindthatseveralcommonlyusedsetsof
sequencetagsordesignmethodologiesusedtoproducesequencetagsdonotmeettheminimumexpectationsoftheir
underlyingdistancemetric,andwefindthatPCRprimersandsequencingadaptersincorporatingeditmetricsequencetags
designedbyoursoftwarepackageperformaswellastheircommercialcounterparts.Wesuggestthatresearchersevaluate
sequencetagspriortouseorevaluatetagsthattheyhavebeenusing.Thesequencetagsetswedesignimproveonextant
sets because they are large, valid across the set, and robust to the suite of sub
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