Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
2008
Improved RNA Alignment Method Using Structural Information
publication
Evidence: high
Author Information
Author(s): Katoh Kazutaka, Toh Hiroyuki
Primary Institution: Kyushu University
Hypothesis
Can incorporating structural information into RNA alignment methods improve their accuracy?
Conclusion
The new X-INS-i method significantly outperforms existing RNA alignment methods in terms of accuracy.
Supporting Evidence
- X-INS-i outperformed other methods in the sum-of-pairs score criterion.
- The accuracy of the present method is comparable to or higher than leading methods like RNA Sampler.
- The method can be used with any combination of algorithms for pairwise RNA alignment.
Takeaway
This study created a new way to align RNA sequences that uses their structures, making the alignments more accurate.
Methodology
The study developed a new RNA alignment framework called X-INS-i, which uses pairwise structural alignments and a new objective function called Four-way Consistency.
Limitations
The method does not consider pseudoknots and relies on external programs for structure prediction.
Statistical Information
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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