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An Improved Search Algorithm for Optimal Multiple-Sequence Alignment
, 2011 Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to push the limits ...
Schroedl, S.
core +1 more source
A multiple sequence alignment program
Nucleic Acids Research, 1986 A program is described for simultaneously aligning two or more molecular sequences which is based on first finding common segments above a specified length and then piecing these together to maximize an alignment scoring function. Optimal as well as near-optimal alignments are found, and there is also provided a means for randomizing the given ...
Eric M. Sobel, Hugo M. Martinez
openaire +4 more sources
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
Bioinform., 2016 Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over ...
K. Katoh, D. Standley
semanticscholar +1 more source
Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences
AlgorithmsThe standard approach for constructing a phylogenetic tree from a set of sequences consists of two key stages. First, a multiple sequence alignment (MSA) of the sequences is computed.
Mahbubeh Askari Rad +2 more
doaj +1 more source
Parallel progressive multiple sequence alignment on reconfigurable meshes
BMC Genomics, 2011 Background One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance.
Nguyen Ken D, Pan Yi, Nong Ge
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Pairwise heuristic sequence alignment algorithm based on deep reinforcement learning [PDF]
arXiv, 2020 Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the traditional sequence alignment method is considerably complicated in proportion to the sequences' length, and it is ...
arxiv
Integrated multiple sequence alignment [PDF]
, 2005 Sammeth M. Integrated multiple sequence alignment. Bielefeld (Germany): Bielefeld University; 2005.The thesis presents enhancements for automated and manual multiple sequence alignment: existing alignment algorithms are made more easily accessible and ...
Sammeth, Michael
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Heuristic for Solving the Multiple Alignment Sequence Problem
Revista de Matemática: Teoría y Aplicaciones, 2011 In this paper we developed a new algorithm for solving the problem of multiple sequence alignment (AM S), which is a hybrid metaheuristic based on harmony search and simulated annealing.
Roman Anselmo Mora Gutiérrez +2 more
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An improved scoring matrix for multiple sequence alignment [PDF]
Mathematical Problems in Engineering, Vol. 2012, No. 490649, pp.
1-9, 2012, 2014 The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper addresses this issue by introducing the concept of joint
arxiv +1 more source
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
BMC Bioinformatics, 2006 Background Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch-like pairwise alignment methods. We introduce a new tool, Sigma, with a new
Siddharthan Rahul
doaj +1 more source