ArticleBioinformatics (Oxford, England)2015
Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- A conserved class of viral RNA structures regulates translation reinitiation through dynamic ribosome interactions.Cell reports · 2025Article
- Diversity and modularity of tyrosine-accepting tRNA-like structures.RNA (New York, N.Y.) · 2024Article
- Efficient 3'-pairing renders microRNA targeting less sensitive to mRNA seed accessibility.Nucleic acids research · 2023Article
- RNA:RNA interaction in ternary complexes resolved by chemical probing.RNA (New York, N.Y.) · 2023Article
- An expanded class of histidine-accepting viral tRNA-like structures.RNA (New York, N.Y.) · 2021Article
- Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity.Science advances · 2021Article
- Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses.RNA (New York, N.Y.) · 2021Article
- An RNA pseudoknot stimulates HTLV-1RNA (New York, N.Y.) · 2020Article
- Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels.Nature communications · 2018Article
- Allosteric mechanism of theeLife · 2018Article
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs.Nature communications · 2018Article
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Authors and funding
6 authors.
Funding
Abstract
motivationCapillary electrophoresis (CE) is a powerful approach for structural analysis of nucleic acids, with recent high-throughput variants enabling three-dimensional RNA modeling and the discovery of new rules for RNA structure design. Among the steps composing CE analysis, the process of finding each band in an electrophoretic trace and mapping it to a position in the nucleic acid sequence has required significant manual inspection and remains the most time-consuming and error-prone step. The few available tools seeking to automate this band annotation have achieved limited accuracy and have not taken advantage of information across dozens of profiles routinely acquired in high-throughput measurements.
resultsWe present a dynamic-programming-based approach to automate band annotation for high-throughput capillary electrophoresis. The approach is uniquely able to define and optimize a robust target function that takes into account multiple CE profiles (sequencing ladders, different chemical probes, different mutants) collected for the RNA. Over a large benchmark of multi-profile datasets for biological RNAs and designed RNAs from the EteRNA project, the method outperforms prior tools (QuSHAPE and FAST) significantly in terms of accuracy compared with gold-standard manual annotations. The amount of computation required is reasonable at a few seconds per dataset. We also introduce an 'E-score' metric to automatically assess the reliability of the band annotation and show it to be practically useful in flagging uncertainties in band annotation for further inspection. AVAILABILITY AND IMPLEMENTATION: The implementation of the proposed algorithm is included in the HiTRACE software, freely available as an online server and for download at http://hitrace.stanford.edu. CONTACT: sryoon@snu.ac.kr or rhiju@stanford.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.