Ribovore is a suite of tools for detecting, classifying and analyzing small subunit ribosomal RNA (SSU rRNA) and large subunit (LSU) rRNA sequences. It is used by GenBank to validate incoming 16S SSU rRNA sequences and to generate high quality datasets of SSU and LSU rRNA sequences for RefSeq and for use as blastn databases. Ribovore is written in Perl.
The ribotyper program is used to
quickly validate and classify rRNA sequences using profile models of
SSU and LSU rRNA genes from different taxonomic groups.
The ribosensor script also
validates and classifies rRNA sequences, but uses blastn to do
single-sequence comparisons in addition to using profiles.
The riboaligner script is used
to check if rRNA sequences are full length and do not extend past the
gene boundary.
The ribodbmaker script performs
a series of tests on input rRNA sequences to create a high quality dataset
of sequences that pass all tests.
- Ribovore installation instructions
ribotyperexample usage, command-line options and unexpected feature informationribosensorexample usage, command-line options and pass/fail criteriariboalignerexample usage, command-line options and length classesribodbmakerexample usage and command-line options- Ribovore model information
- The recommended citation for using ribovore is: Alejandro A. Schaffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly Underwood, Ilene Karsch-Mizrachi, Eric P. Nawrocki; Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation; in preparation (to be uploaded to bioRxiv in Feb 2021);