Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation

BMC Bioinformatics

Table 7 Mapping of GenBank errors to the rRNA_sensor and ribotyper errors that trigger them

GenBank error	Fails to	Triggering rRNA_sensor/ribotyper errors
SEQ_HOM_NotSSUOrLSUrRNA	Submitter	S_NoHits^*, R_NoHits
SEQ_HOM_LowSimilarity	Submitter	S_NoSimilarity^, S_LowSimilarity^, S_LowScore^*, R_LowScore
SEQ_HOM_SSUAndLSUrRNA	Submitter	R_MultipleFamilies
SEQ_HOM_MisAsBothStrands	Submitter	S_BothStrands, R_BothStrands
SEQ_HOM_MisAsHitOrder	Submitter	R_InconsistentHits
SEQ_HOM_MisAsDupRegion	Submitter	R_DuplicateRegion
SEQ_HOM_TaxNotExpectedSSUrRNA	Submitter	R_UnacceptableModel
SEQ_HOM_TaxQuestionableSSUrRNA	Indexer	R_QuestionableModel⁺
SEQ_HOM_LowCoverage	Indexer	R_LowCoverage
SEQ_HOM_MultipleHits	Indexer	S_MultipleHits, R_MultipleHits⁺

There are two classes of exceptions marked by two different superscripts in the table: ‘*’: these rRNA_sensor errors do not trigger a GenBank error if: (a) the sequence is ’RPSF’ (passes ribotyper and fails rRNA_sensor) and the -c option is not used with ribosensor. or (b) the sequence is ’RFSF’ (fails both ribotyper and rRNA_sensor) and R_UnacceptableModel or R_QuestionableModel are also reported. ‘+’: these ribotyper errors do not trigger a GenBank error if sequence is ’RFSP’ (fails ribotyper and passes rRNA_sensor)

ISSN: 1471-2105