A fast structural multiple alignment method for long RNA sequences
By Yasuo Tabei, H. Kiryu, Taishin Kin, Kiyoshi Asai. 2008
114 citations recorded by the source corpus.
BackgroundAligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been proposed, they are either inaccurate or computationally too expensive. Faster methods with reasonable accuracies are required for genome-scale analyses.ResultsWe propose a fast algorithm for multiple structural alignments of RNA sequences that is an extension of our pairwise structural alignment method (implemented in SCARNA). The accuracies of the implemented software, MXSCARNA, are at least as favorable as those of state-of-art algorithms that are computationally much more expensive in time and memory.ConclusionThe proposed method for structural alignment of multiple RNA sequences is fast enough for large-scale analyses with accuracies at least comparable to those of existing algorithms. The source code of MXSCARNA and its web server are available at http://mxscarna.ncrna.org.
Subfields: Molecular Biology
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In Molecular Biology
- Kazutaka Katoh
- Hiroyuki Toh
- Patrick Kück
- H. Letsch
- Roman R. Stocsits
- Byung-Jun Yoon
- Sayed Mohammad Ebrahim Sahraeian
- Bernhard Misof
Citations in the corpus
- 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): “We used as structure informed alignment programs: 1) MXSCARNA (Tabei et al. 2008), which is a multiple sequence alignment version of SCARNA (Tabei et al. 2006).”
- PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach (2011, methodology): “Thus, Wang et al. [44] These results confirm that PicXAA-R can efficiently yield an accurate structural alignment for a set of large number of locally similar RNAs.”
- Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, methodology): “As representatives of the exiting methods, we selected the five latest methods, Murlet [10], MXSCARNA [14], RNA Sampler [11], LaRA [9] and MASTR [13], which reportedly outperformed the other methods, including FoldalignM [8], RNAcast [3], Dynalign [2] and Stemloc [4], consistently.”