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

BMC Bioinformatics

Table 5 Descriptions of rRNA_sensor errors within ribosensor and mapping to the GenBank errors they trigger

rRNA_sensor error	Associated GenBank error	Cause/explanation
S_NoHits^*	SEQ_HOM_NotSSUOrLSUrRNA	No hits reported (‘no’ column 2)
S_NoSimilarity^*	SEQ_HOM_LowSimilarity	Coverage (column 5) of best blast hit is < 10%
S_LowSimilarity^*	SEQ_HOM_LowSimilarity	Coverage (column 5) of best blast hit is < 80% (≤ 350 nt) or 86% (> 350 nt)
S_LowScore^*	SEQ_HOM_LowSimilarity	Either id percentage below length-dependent threshold (75%, 80%, 86%) or E-value above 1e−40 (’imperfect_match’ column 2)
S_BothStrands	SEQ_HOM_MisAsBothStrands	Hits on both strands (’mixed’ column 2)
S_MultipleHits	SEQ_HOM_MultipleHits	More than 1 hit reported (column 4 > 1)

‘*’: The first four rRNA_sensor errors do not trigger GenBank errors and are ignored by ribosensor if either (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 ribotyper errors are also reported

ISSN: 1471-2105