WMSA: a novel method for multiple sequence alignment of DNA sequences

• DOI: 10.1093/bioinformatics/btac658
• Publication Date: 2022-09-29T20:48:12Z
• Authors: Yanming Wei; Quan Zou; Furong Tang; Liang Yu
• Keywords: Multiple sequence alignment; Sequence (biology); Code (set theory); Alignment-free sequence analysis

Abstract Motivation Multiple sequence alignment (MSA) is a fundamental problem in bioinformatics. The quality of will affect downstream analysis. MAFFT has adopted the Fast Fourier Transform method for searching homologous segments and using them as anchors to divide sequences, then making only on segments, which can save time memory without overly reducing quality. becomes slow when dataset large. Results We made software, WMSA, uses divide-and-conquer split sequences into clusters, aligns those clusters profiles with center star strategy makes progressive profile–profile alignment. conducted by compiled algorithms MAFFT, K-Band multithread parallelism. Our balance time, space performs better than test experiments highly conserved datasets. Availability implementation Source code freely available at https://github.com/malabz/WMSA/, implemented C/C++ supported Linux, datasets are https://github.com/malabz/WMSA-dataset. Supplementary information data Bioinformatics online.