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

Background: Structural 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. Results: We 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 pai...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Kazutaka Katoh, Hiroyuki Toh
• Keywords: BMCBI 2008, Multiple Alignment, Multiple Rna Alignment, Structural Alignments