RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment

Bayegan, Amir H.; Clote, Peter

doi:10.1371/journal.pone.0227177

Cited by 4 publications

(7 citation statements)

References 53 publications

(111 reference statements)

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“…We generated networks comprised of vertices corresponding to individual glycine riboswitch aptamers with edges weighted based on the pairwise RNAmountAlign distance score [34]. RNAmountAlign was chosen as the primary metric for edge-weighting in our work due to its implemented use of primary sequence information and ensemble mountain distance of secondary structure to generate a pairwise score more quickly and efficiently than other software.…”

Section: Genomic Context Dictates Aptamer Clustering In Bacillaceae Amentioning

confidence: 99%

“…Aptamer networks were generated to determine clustering based on a number of different pairwise metrics. These included partition function (RNApdist) [26,27], sequence and structural similarity (FoldAlign and Dynalign) [30][31][32][33], ensemble expected mountain height (RNAmountAlign) [34], and sequence similarity (Clustal Omega) [28]. Pairwise values were utilized to generate and visualize aptamer networks using the igraph and qgraph R-libraries [76,77].…”

Section: Graph Clustering and Network Generationmentioning

confidence: 99%

“…Our approach allows any measure of pairwise similarity between two RNA sequences to be utilized for comparison and relative conservation between groups to be investigated. Thus, measures that incorporate purely secondary structure information [26,27], purely sequence information [28,29], or a combination of both [30][31][32][33][34], may be utilized so that all available information can be captured. While this approach does not yield the same kind of inferences concerning the line of descent as traditional phylogenetic approaches, it does enable many more variables to be accounted for while assessing ncRNA similarity.…”

Section: Introductionmentioning

confidence: 99%

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Regulatory context drives conservation of glycine riboswitch aptamers

2019

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In comparison to protein coding sequences, the impact of mutation and natural selection on the sequence and function of non-coding (ncRNA) genes is not well understood. Many ncRNA genes are narrowly distributed to only a few organisms, and appear to be rapidly evolving. Compared to protein coding sequences, there are many challenges associated with assessment of ncRNAs that are not well addressed by conventional phylogenetic approaches, including: short sequence length, lack of primary sequence conservation, and the importance of secondary structure for biological function. Riboswitches are structured ncRNAs that directly interact with small molecules to regulate gene expression in bacteria. They typically consist of a ligand-binding domain (aptamer) whose folding changes drive changes in gene expression. The glycine riboswitch is among the most well-studied due to the widespread occurrence of a tandem aptamer arrangement (tandem), wherein two homologous aptamers interact with glycine and each other to regulate gene expression. However, a significant proportion of glycine riboswitches are comprised of single aptamers (singleton). Here we use graph clustering to circumvent the limitations of traditional phylogenetic analysis when studying the relationship between the tandem and singleton glycine aptamers. Graph clustering enables a broader range of pairwise comparison measures to be used to assess aptamer similarity. Using this approach, we show that one aptamer of the tandem glycine riboswitch pair is typically much more highly conserved, and that which aptamer is conserved depends on the regulated gene. Furthermore, our analysis also reveals that singleton aptamers are more similar to either the first or second tandem aptamer, again based on the regulated gene. Taken together, our findings suggest that tandem glycine riboswitches degrade into functional singletons, with the regulated gene(s) dictating which glycine-binding aptamer is conserved.

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Section: Genomic Context Dictates Aptamer Clustering In Bacillaceae Amentioning

confidence: 99%

Section: Graph Clustering and Network Generationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Regulatory context drives conservation of glycine riboswitch aptamers

2019

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“…In order to compute the MCC (Eq. 1), we follow the publications of Murlet [48] and RNAmountAlign [32]. For future reference and reproducibility we provide the script in our LaRA 2 repository.…”

Section: Benchmark On General Rna Familiesmentioning

confidence: 99%

“…For a complete overview of all tools related to sequence-structure alignment we refer to the review paper by Lalwani et al [31]. A recent paper in this field introduced a new tool RNAmountAlign [32] which uses mountain distance for pairwise structural alignments and runs in O(n 3 ) time for sequences of length n. The paper demonstrates besides RNAmountAlign also good performance for LocARNA [6] and LaRA [5]. LocARNA implements a variant of Sankoff 's algorithm and is based on computing pairwise local Fig.…”

mentioning

confidence: 99%

LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences

et al. 2022

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Background The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson–Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. Results We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. Conclusions With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases.

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RNA threading with secondary structure and sequence profile

Du,

Peng,

Yang

2024

Bioinformatics

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Motivation RNA threading aims to identify remote homologies for template-based modeling of RNA 3D structure. Existing RNA alignment methods primarily rely on secondary structure alignment. They are often time- and memory-consuming, limiting large-scale applications. In addition, the accuracy is far from satisfactory. Results Using RNA secondary structure and sequence profile, we developed a novel RNA threading algorithm, named RNAthreader. To enhance the alignment process and minimize memory usage, a novel approach has been introduced to simplify RNA secondary structures into compact diagrams. RNAthreader employs a two-step methodology. Initially, integer programming and dynamic programming are combined to create an initial alignment for the simplified diagram. Subsequently, the final alignment is obtained using dynamic programming, taking into account the initial alignment derived from the previous step. The benchmark test on 80 RNAs illustrates that RNAthreader generates more accurate alignments than other methods, especially for RNAs with pseudoknots. Another benchmark, involving 30 RNAs from the RNA-Puzzles experiments, exhibits that the models constructed using RNAthreader templates have a lower average root mean square deviation (RMSD) than those created by alternative methods. Remarkably, RNAthreader takes less than two hours to complete alignments with ∼5000 RNAs, which is 3∼40 times faster than other methods. These compelling results suggest that RNAthreader is a promising algorithm for RNA template detection. Availability https://yanglab.qd.sdu.edu.cn/RNAthreader Supplementary information Supplementary data are available at Bioinformatics online.

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RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment

Cited by 4 publications

References 53 publications

Regulatory context drives conservation of glycine riboswitch aptamers

Regulatory context drives conservation of glycine riboswitch aptamers

LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences

RNA threading with secondary structure and sequence profile

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