Rfam: updates to the RNA families database

Area of Science:

• Bioinformatics
• Genomics
• Molecular Biology

Background:

• Rfam is a curated database of RNA sequence families.
• It utilizes multiple sequence alignments and covariance models (CMs) for RNA identification.
• Current annotation efforts focus on identifying known RNA families within nucleotide sequences.

Purpose of the Study:

• To describe recent improvements to the Rfam database.
• To highlight advancements in Rfam's website, methodologies, and data.
• To facilitate the annotation of RNA sequences in genomes.

Main Methods:

• Utilizing BLAST filters in conjunction with covariance models (CMs) for sensitive RNA family annotation.
• Analyzing taxonomic range and annotation yield for different RNA families (e.g., tRNA, rRNA, snoRNAs, miRNAs).
• Implementing recent updates to Rfam's computational infrastructure and data curation processes.

Main Results:

• A minority of broad-range RNA families (tRNA, rRNA) contribute the majority of annotations.
• The majority of Rfam families (snoRNAs, miRNAs) have limited taxonomic distribution and annotation output.
• Recent improvements have enhanced the Rfam website, methodologies, and data quality.

Conclusions:

• Rfam serves as a crucial resource for RNA sequence annotation.
• Ongoing improvements ensure Rfam remains a leading database for RNA discovery.
• The database is freely accessible online for researchers worldwide.