ArticleCurrent protocols in bioinformatics2016
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.
Article in Current protocols in bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
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- TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts.NAR genomics and bioinformatics · 2024Article
- Identification and Characterization of Non-protein Coding RNA Homologs inIndian journal of microbiology · 2024Article
- Small regulatory RNAs are mediators of theJournal of bacteriology · 2023Article
- GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context.GigaScience · 2022Article
- Genome-Wide Identification of Novel sRNAs in Streptococcus mutans.Journal of bacteriology · 2022Article
- A Peroxide-Responding sRNA Evolved from a Peroxidase mRNA.Molecular biology and evolution · 2022Article
- Ms1 RNA Interacts With the RNA Polymerase Core inFrontiers in microbiology · 2022Article
- Review
- Monophyletic Origin and Divergent Evolution of Animal Telomerase RNA.Molecular biology and evolution · 2021Article
- Complete Genome Sequence of Burkholderia cenocepacia K56-2, an Opportunistic Pathogen.Microbiology resource announcements · 2020Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
- Computational search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo ecosystems.PloS one · 2019Article
- Non-Coding RNA Analysis Using the Rfam Database.Current protocols in bioinformatics · 2018Article
- High-throughput sequencing identification and characterization of potentially adhesion-related small RNAs in Streptococcus mutans.Journal of medical microbiology · 2018Article
- Genome annotation for clinical genomic diagnostics: strengths and weaknesses.Genome medicine · 2017Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
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.
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