ArticleBioinformatics (Oxford, England)2015
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.
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 25 papers.
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Who cites it
25 citing papers in PubMed.
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- REDalign: accurate RNA structural alignment using residual encoder-decoder network.BMC bioinformatics · 2024Article
- DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning.Journal of chemical information and modeling · 2024Article
- LocARNA 2.0: Versatile Simultaneous Alignment and Folding of RNAs.Methods in molecular biology (Clifton, N.J.) · 2024Article
- ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring.Bioinformatics (Oxford, England) · 2023Article
- Network-Based Structural Alignment of RNA Sequences Using TOPAS.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Informative RNA base embedding for RNA structural alignment and clustering by deep representation learning.NAR genomics and bioinformatics · 2022Article
- LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.BMC bioinformatics · 2022Article
- SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability.Computational and structural biotechnology journal · 2022Article
- Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans.Database : the journal of biological databases and curation · 2021Article
- DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data.Frontiers in genetics · 2021Article
- aliFreeFoldMulti: alignment-free method to predict secondary structures of multiple RNA homologs.NAR genomics and bioinformatics · 2020Article
- Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.Algorithms for molecular biology : AMB · 2020Article
- The locality dilemma of Sankoff-like RNA alignments.Bioinformatics (Oxford, England) · 2020Article
- RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency.RNA (New York, N.Y.) · 2020Article
- GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering.GigaScience · 2019Article
- Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS.Molecules (Basel, Switzerland) · 2019Article
- Freiburg RNA tools: a central online resource for RNA-focused research and teaching.Nucleic acids research · 2018Article
- aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences.Bioinformatics (Oxford, England) · 2018Article
- TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.Nucleic acids research · 2017Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationRNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of [Formula: see text]. Subsequently, numerous faster 'Sankoff-style' approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks down for RNAs with sequence identities below 60%. Alignment approaches like LocARNA that do not require sequence-based heuristics, have been limited to high complexity ([Formula: see text] quartic time).
resultsBreaking this barrier, we introduce the novel Sankoff-style algorithm 'sparsified prediction and alignment of RNAs based on their structure ensembles (SPARSE)', which runs in quadratic time without sequence-based heuristics. To achieve this low complexity, on par with sequence alignment algorithms, SPARSE features strong sparsification based on structural properties of the RNA ensembles. Following PMcomp, SPARSE gains further speed-up from lightweight energy computation. Although all existing lightweight Sankoff-style methods restrict Sankoff's original model by disallowing loop deletions and insertions, SPARSE transfers the Sankoff algorithm to the lightweight energy model completely for the first time. Compared with LocARNA, SPARSE achieves similar alignment and better folding quality in significantly less time (speedup: 3.7). At similar run-time, it aligns low sequence identity instances substantially more accurate than RAF, which uses sequence-based heuristics.
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