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Rfam 12.0: updates to the RNA families database
Eric P Nawrocki1, Sarah W Burge2, Alex Bateman2
1HHMI Janelia Farm Research Campus, Ashburn, VA, USA.
Nucleic Acids Research
|November 14, 2014
Summary
The Rfam database now features an upgraded search pipeline for improved non-coding RNA (ncRNA) homology detection. This release enhances RNA annotation capabilities and expands the Rfam collection with new families and motif information.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- The Rfam database is a curated resource for non-coding RNA (ncRNA) families.
- It provides sequence alignments, secondary structures, and annotations from various resources.
- Previous versions relied on older search methodologies.
Purpose of the Study:
- To detail updates and improvements in the Rfam database and website for release 12.0.
- To introduce an upgraded search pipeline using Infernal 1.1 for enhanced homology detection.
- To expand the Rfam collection and incorporate new types of RNA information.
Main Methods:
- Upgraded the Rfam search pipeline to utilize Infernal 1.1.
- Compared the performance of the new Infernal 1.1 pipeline against the previous version.
- Applied the new pipeline for annotating RNAs in diverse genomic and metagenomic datasets.
Main Results:
- Demonstrated improved homology detection capabilities with the Infernal 1.1 pipeline.
- The new pipeline offers enhanced usability for users analyzing their own datasets.
- Rfam 12.0 includes 260 new families, notably the large subunit ribosomal RNA family.
- Introduced information on short sequence- and structure-based RNA motifs within families.
Conclusions:
- The upgraded Rfam pipeline significantly improves ncRNA identification and annotation.
- Rfam 12.0 provides a more comprehensive and user-friendly resource for RNA research.
- The inclusion of new families and motif data expands the scope of discoverable RNA elements.
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