FAMSA: Fast and accurate multiple sequence alignment of huge protein families [PDF]
Scientific Reports, 2016 Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment ...
Sebastian Deorowicz +2 more
semanticscholar +1 more source
Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure [PDF]
, 2013 Background: Most phylogeny analysis methods based on molecular sequences use multiple alignment where the quality of the alignment, which is dependent on the alignment parameters, determines the accuracy of the resulting trees.
Bakis, Yasin +11 more
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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Molecular Systems Biology, 2011 Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets
Fabian Sievers +11 more
semanticscholar +1 more source
Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing [PDF]
, 2003 Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological
Gilbert, D, Westhead, DR, Williams, A
core +1 more source
Protein Multiple Sequence Alignment [PDF]
, 2008 Protein sequence alignment is the task of identifying evolutionarily or structurally related positions in a collection of amino acid sequences. Although the protein alignment problem has been studied for several decades, many recent studies have demonstrated considerable progress in improving the accuracy or scalability of multiple and pairwise ...
Kazutaka Katoh, Chuong B. Do
openaire +3 more sources
Score distributions of gapped multiple sequence alignments down to the low-probability tail [PDF]
Phys. Rev. E 94, 022127 (2016), 2015 Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small.
arxiv +1 more source
Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450 [PDF]
, 2006 Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection.
Arnold, Frances H. +5 more
core +1 more source
Current Trends and Ongoing Progress in the Computational Alignment of Biological Sequences
IEEE Access, 2019 The computational techniques for nucleic acid and protein sequence comparison reduce the extensive burden of molecular biologists. The sequence alignment is one of the main research areas in bioinformatics, and comparative genomics and proteomics lead us
Muhammad Ishaq +3 more
doaj +1 more source
CLUSTAL V: improved software for multiple sequence alignment
Comput. Appl. Biosci., 1992 The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on any machine with a standard C compiler.
D. Higgins, A. Bleasby, R. Fuchs
semanticscholar +1 more source
BMC Bioinformatics, 2020 Background Given a binary tree T $\mathcal {T}$ of n leaves, each leaf labeled by a string of length at most k, and a binary string alignment function ⊗, an implied alignment can be generated to describe the alignment of a dynamic homology for T ...
Alex J. Washburn, Ward C. Wheeler
doaj +1 more source