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

BMC Bioinformatics

Table 8 NCBI rRNA and ITS sequence submission types and attributes

Submission type	Submission subtype	Validation method	Percentage of accepted submissions	Percentage of accepted sequences
Prokaryotic rRNA/IGS	SSU rRNA only (16S) ≥ 2500 seqs	ribosensor	0.648%	99.604%
	SSU rRNA only (16S) < 2500 seqs	blastn(ribo)	43.934%	0.1252%
	LSU rRNA only (23S)	blastn(ribo)	0.754%	0.0027%
	intergenic spacer (16S-23S IGS)	blastn	(sum of 2 rows)
Eukaryotic Nuclear rRNA/ITS	Contains rRNA-ITS region	blastn	54.663%	0.2682%
	SSU rRNA only (18S)	blastn(ribo)	(sum of 8 eukaryotic rows)
	LSU rRNA only (28S)	blastn(ribo)
	ITS1 only	blastn
	ITS2 only	blastn
Eukaryotic Organellar rRNA	Mitochondrial SSU rRNA (12S)	blastn
	Mitochondrial LSU rRNA (16S)	blastn
	Chloroplast SSU rRNA (16S)	blastn
	Chloroplast LSU rRNA (23S)	blastn

The ’submission type’ column indicates the three possible rRNA sequence related options for GenBank submissions available at https://submit.ncbi.nlm.nih.gov/subs/genbank/. There is not an intergenic spacer type of eukaryotes at this time. The ’submission subtype’ column indicates the more specific possible sequence types a submitter can select after choosing one of the options in the first column. The ’validation method’ column indicates whether incoming sequences are processed with ribosensor, blastn using a database constructed with ribodbmaker (’blast(ribo)’) or blastn using either the general non-redundant (nr) database or a database constructed by other means (’blastn’). The ’percentage of accepted submissions’ and ’percentage of accepted sequences’ reflect rRNA/IGS/ITS submissions published between Jan 1, 2020 and May 31, 2020. Note that the percentages for rows 3 and 4 are summed and reported in row 3, and for rows 5 through 12 (all eukaryotic submission types) are summed and reported in in row 5. Counts pertain only to submissions that advanced through enough preliminary checks to be assigned an internal submission code

ISSN: 1471-2105