2021/01/01 by Eloi Araujo, Elói Araújo, Luiz Rozante +4
Biochemistry, Genetics and Molecular Biology · Computer Science · #Algorithm #Algorithms and Data Compression #Alignment-free sequence analysis #Artificial intelligence #Biology #Computer science #Data Mining Algorithms and Applications #Genomics and Phylogenetic Studies #Multiple sequence alignment #Normalization (sociology) #Pairwise comparison #Pattern recognition (psychology) #Peptide sequence #Sequence (biology) #Sequence alignment #acm:68W25 #cs.DS #msc:68W25
paper · pdf · doi:10.4230/lipics.isaac.2021.40
24 pages, 2 figures, 5 algorithms
openalex publication_date 2021/01/01 · arxiv created 2021/12/03 · arxiv updated 2021/12/06 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and other fields. While the alignment of two sequences may be performed swiftly in many applications, the simultaneous alignment of multiple sequences proved to be naturally more intricate. Although most multiple sequence alignment (MSA) formulations are NP-hard, several approaches have been developed, as they can outperform pairwise alignment methods or are necessary for some applications. Taking into account not only similarities but also the lengths of the compared sequences (i.e. normalization) can provide better alignment results than both unnormalized or post-normalized approaches. While some normalized methods have been developed for pairwise sequence alignment, none have been proposed for MSA. This work is a first effort towards the development of normalized methods for MSA. We discuss multiple aspects of normalized multiple sequence alignment (NMSA). We define three new criteria for computing normalized scores when aligning multiple sequences, showing the NP-hardness and exact algorithms for solving the NMSA using those criteria. In addition, we provide approximation algorithms for MSA and NMSA for some classes of scoring matrices.