ArticleRNA (New York, N.Y.)2009
The tedious task of finding homologous noncoding RNA genes.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
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- Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning.Briefings in bioinformatics · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
- RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation.bioRxiv : the preprint server for biology · 2025Article
- Unbiased anchors for reliable genome-wide synteny detection.Algorithms for molecular biology : AMB · 2025Article
- Multiple sequence alignment-based RNA language model and its application to structural inference.Nucleic acids research · 2024Article
- GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context.GigaScience · 2022Article
- Does rapid sequence divergence preclude RNA structure conservation in vertebrates?Nucleic acids research · 2022Article
- The Genome of the "Sea Vomit"Life (Basel, Switzerland) · 2021Article
- A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions.Bioinformatics (Oxford, England) · 2021Article
- Article
- The locality dilemma of Sankoff-like RNA alignments.Bioinformatics (Oxford, England) · 2020Article
- Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function.Nucleic acids research · 2019Article
- BC200 (BCYRN1) - The shortest, long, non-coding RNA associated with cancer.Non-coding RNA research · 2018Review
- Detailed secondary structure models of invertebrate 7SK RNAs.RNA biology · 2018Article
- GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence.Frontiers in genetics · 2018Article
- RNAlien - Unsupervised RNA family model construction.Nucleic acids research · 2016Article
- Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.Current protocols in bioinformatics · 2016Article
- RNA motif discovery: a computational overview.Biology direct · 2015Review
- The Expansion of Animal MicroRNA Families Revisited.Life (Basel, Switzerland) · 2015Article
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3 authors.
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Abstract
User-driven in silico RNA homology search is still a nontrivial task. In part, this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent, computational costs are still problematic in practice. An important, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain, not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging: BLAST still works better or equally good as other methods unless extensive expert knowledge on the RNA family is included. However, when good curated data are available the recent development yields further improvements in finding remote homologs. Homology search beyond the reach of BLAST hence is not at all a routine task.
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