Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families. Issue 1 (20th June 2016)

• Record Type: Journal Article
• Authors: Barquist, Lars; Burge, Sarah W.; Gardner, Paul P.
• Editors: Bateman, Alex; Pearson, William R.; Stein, Lincoln D.; Stormo, Gary D.; Yates, John R.
• Is Part Of: Current protocols in bioinformatics. Volume 54:Issue 1(2016)
• Page Start: 12.13.1
• Page End: 12.13.25
• Publication Date: 2016-06-20
• Subjects: covariance model -- homology -- RNA -- Rfam -- alignment -- ncRNA -- conservation; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.4
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: Emerging high‐throughput technologies have led to a deluge of putative non‐coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology detection is critical to making maximal use of functional information gathered about ncRNAs: identifying homologous sequence allows us to transfer information gathered in one organism to another quickly and with a high degree of confidence. ncRNA presents a challenge for homology detection, as the primary sequence is often poorly conserved and de novo secondary structure prediction and search remain difficult. This unit introduces methods developed by the Rfam database for identifying "families" of homologous ncRNAs starting from single "seed" sequences, using manually curated sequence alignments to build powerful statistical models of sequence and structure conservation known as covariance models (CMs), implemented in the Infernal software package. We provide a step‐by‐step iterative protocol for identifying ncRNA homologs and then constructing an alignment and corresponding CM. We also work through an example for the bacterial small RNA MicA, discovering a previously unreported family of divergent MicA homologs in genus Xenorhabdus in the process. © 2016 by John Wiley & Sons, Inc.