ArticlePloS one2020
RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- REDalign: accurate RNA structural alignment using residual encoder-decoder network.BMC bioinformatics · 2024Article
- RNA threading with secondary structure and sequence profile.Bioinformatics (Oxford, England) · 2024Article
- Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction.PLoS computational biology · 2023Article
- LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.BMC bioinformatics · 2022Article
- Regulatory context drives conservation of glycine riboswitch aptamers.PLoS computational biology · 2019Article
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2 authors.
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Abstract
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural homology identification. This paper describes C++ software, RNAmountAlign, for RNA sequence/structure alignment that runs in O(n3) time and O(n2) space for two sequences of length n; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics for local alignment, as well as parameter fitting for local and global alignment. Using incremental mountain height, a representation of structural information computable in cubic time, RNAmountAlign implements quadratic time pairwise local, global and global/semiglobal (query search) alignment using a weighted combination of sequence and structural similarity. RNAmountAlign is capable of performing progressive multiple alignment as well. Benchmarking of RNAmountAlign against LocARNA, LARA, FOLDALIGN, DYNALIGN, STRAL, MXSCARNA, and MUSCLE shows that RNAmountAlign has reasonably good accuracy and faster run time supporting all alignment types. Additionally, our extension of RNAmountAlign, called RNAmountAlignScan, which scans a target genome sequence to find hits having high sequence and structural similarity to a given query sequence, outperforms RSEARCH and sequence-only query scans and runs faster than FOLDALIGN query scan.
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