Skip to main content

Table 4 Attributes of the 16 types of ribotyper unexpected features

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

Unexpected feature name

Description

NoHits*

No stage 1 hits above threshold to any models

UnacceptableModel*

Best stage 1 hit is to a model that is unacceptable as defined in --inaccept input file

MultipleFamilies*

Stage 1 hits exist to more than one family (e.g. SSU and LSU)

BothStrands*

Stage 1 hits above threshold exist on both strands

DuplicateRegion*

At least two stage 1 or 2 hits on same strand overlap

InconsistentHits*

Not all hits are in the same order in sequence and model coordinates

QuestionableModel*

Best stage 1 hit is to a model that is questionable as defined in --inaccept input file

MinusStrand

Best stage 1 hit is on the minus strand

LowScore

The bits per nucleotide value (total bit score divided by total length of sequence) is below threshold of 0.50

LowCoverage

Sequence coverage of all hits is below threshold of 0.86

LowScoreDifference

Difference between top two models in different domains is below 0.10 bits per position

VeryLowScoreDifference

Difference between top two models in different domains is below 0.04 bits per position

MultipleHits

There is more than one hit to the best scoring model on the same strand

EvalueScoreDiscrepancy

If hits were sorted by E-value due to --evalue, best hit has lower bit score than second best hit

TooShort*

Sequence length is less than <n> and --shortfail <n> used

TooLong*

Sequence length is greater than <n> and --shortlong <n> used

  1. Unexpected features labelled with * in the first column are fatal by default, in that they cause a sequence to fail. UnacceptableModel and QuestionableModel can only potentially be reported if the --inaccept option is used. EvalueScoreDiscrepancy can only be reported if the --evalues option is used. TooShort and TooLong can only be reported if the --shortfail or --longfail options are used, respectively