Qing Zhan, Yilei Fu, Qinghua Jiang, Bo Liu, Jiajie Peng and Yadong Wang* Pages 1 - 8 ( 8 )
Background: Multiple sequence alignment (MSA) is a fundamental task in bioinformatics and is required for many biological analysis tasks. The more accurate the alignments are, the more credible the downstream analyses are. Most of the protein MSA algorithms realign alignment to refine it by dividing it into two groups horizontally and realign the two groups. However, this strategy doesn't consider that different regions of the sequences have different conservation, and this property may lead to incorrect residue-residue or residue-gap pairs which could not be corrected by this strategy.
Method: Here, we present a novel refinement method based on splitting-splicing vertically, called SpliVert. For an alignment, we split it vertically into 3 parts, remove the gap characters in the middle part, realign the middle part alone, and splice the realigned middle parts with the other two initial parts together to obtain a refined alignment. In the realign procedure of our methods, the aligner will only focus on the certain part, ignoring the disturbance of the other parts, which could help to fix the incorrect pairs.
Results: We tested our refinement strategy for 2 leading MSA tools on 3 standard benchmarks, according to the commonly used average SP (and TC) score. The results show that given appropriate proportions to split the initial alignment, the average scores are increased comparably or slightly after using our methods. We also compared the alignments refined by our methods with the alignments refined directly by the original alignment tools. The results suggest that using our SpliVert method to refine alignment can also outperform using the original alignment tools directly.
protein, multiple sequence alignment, progressive alignment, realign, refinement, splitting-splicing vertically
School of Computer Science and Technology, Harbin Institute of Technology, Harbin, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, School of Life Science and Technology, Harbin Institute of Technology, Harbin, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, School of Computer Science, Northwestern Polytechnical University, Xi`an, School of Computer Science and Technology, Harbin Institute of Technology, Harbin