Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

By Kazutaka Katoh, Hiroyuki Toh. 2008

602 citations recorded by the source corpus.

BackgroundStructural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized.ResultsWe took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage.ConclusionThe BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.

Subfields: Molecular Biology

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “After reviewing the previous version (version 6) in Katoh and Toh (2008b), we have been continuously improving its accuracy, speed, and utility in practical situations.”
A global molecular phylogeny of 147 periwinkle species (Gastropoda, Littorininae) (2012, methodology): “The Q-INS-i option was used, which is recommended for a global alignment of highly diverged ncRNAs as secondary structure of RNA is considered (Katoh & Toh 2008).”
Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life (2016, methodology): “…B. edulis) and one genome with more than 50% missing data in an initial alignment (Moniliophthora perniciosa) from the data downloaded from JGI, the 210 single copy genes initially targeted were aligned separately using MAFFT, version 6 (Katoh et al., 2002; Katoh & Toh, 2008) under LINS-i settings.”
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach (2011, methodology): “MAFFT-xinsi [26] uses a four-way consistency objective function to progressively build a structural alignment by combining pairwise alignments predicted by an external program.”
The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods. (2010, methodology): “In MXSCARNA, the pairwise structural alignment process is extended to a progressive multiple sequence alignment, 2) X-INS-i (MAFFT, Katoh and Toh 2008), which has been developed to align nc RNA sequences.”
Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming (2011, methodology): “847 taking into account the RNA secondary structure (Q-INS-i option; Katoh and Toh, 2008), then manually refined using BioEdit v7.”