Ribovore

Ribovore validates, classifies, and analyzes small subunit (SSU) and large subunit (LSU) ribosomal RNA sequences, including 16S SSU rRNA, to support GenBank submission validation, RefSeq dataset generation, and BLASTn database construction.

Key Features:

• Sequence validation: Uses programs theribotyper and ribosensor to validate incoming bacterial and archaeal SSU rRNA sequences for GenBank inclusion.
• Database creation: Uses theribodbmaker to assemble high-quality rRNA datasets for RefSeq and for construction of BLASTn rRNA databases.
• Alignment, classification, and validation: Performs alignment, taxonomic classification, and validation of rRNA sequences.
• Profile and structure-aware analysis: Compares sequences against ribosomal RNA profile hidden Markov models (HMMs) and covariance models that account for sequence and secondary-structure conservation.
• BLASTn database maintenance: Maintains nine BLASTn rRNA databases used for sequence verification and for the NCBI BLAST browser.

Scientific Applications:

• GenBank submission screening: Determines which SSU rRNA sequences are likely to pass automated checks for GenBank acceptance.
• RefSeq curation: Supports selection and curation of RefSeq rRNA records, including at least 10,435 fungal rRNA RefSeq records from type material across 8,350 taxa.
• Large-scale rRNA processing: Has been used to process over 50 million prokaryotic SSU rRNA sequences submitted to GenBank since 2018.

Methodology:

Combines single-sequence and profile-based methods to perform alignment, classification, and validation; compares sequences to ribosomal RNA profile HMMs and covariance models that incorporate secondary-structure conservation; implemented in Perl.