Abstract
Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes. Several programs have been developed for identifying RNAs, including specific tools tailored to a particular RNA family as well as more general ones designed to work for any family. Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence, and structure of an RNA family. In this chapter, as an illustrative example, the Infernal software package and CMs from the Rfam database are used to identify RNAs in the genome of the archaeon Methanobrevibacter ruminantium, uncovering some additional RNAs not present in the genome's initial annotation. Analysis of the results and comparison with family-specific methods demonstrate some important strengths and weaknesses of this general approach.
Keywords
Computational biologyGenomeBiologyAnnotationRNANon-coding RNAGeneticsGene
Affiliated Institutions
Related Publications
Rfam 12.0: updates to the RNA families database
The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structu...
Transcriptome-wide discovery of circular RNAs in Archaea
Circular RNA forms had been described in all domains of life. Such RNAs were shown to have diverse biological functions, including roles in the life cycle of viral and viroid ge...
tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences
Transfer RNAs are the largest, most complex non-coding RNA family, universal to all living organisms. tRNAscan-SE has been the de facto tool for predicting tRNA genes in whole g...
Infernal 1.1: 100-fold faster RNA homology searches
Abstract Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated mult...
Rfam 11.0: 10 years of RNA families
The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily...
Publication Info
- Year
- 2013
- Type
- article
- Volume
- 1097
- Pages
- 163-197
- Citations
- 81
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
81
OpenAlex
Cite This
Eric P. Nawrocki
(2013).
Annotating Functional RNAs in Genomes Using Infernal.
Methods in molecular biology
, 1097
, 163-197.
https://doi.org/10.1007/978-1-62703-709-9_9
Identifiers
- DOI
- 10.1007/978-1-62703-709-9_9