Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding. [PDF]
Bioinformatics, 2023 Liu Y +6 more
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Data set of phylogenetic analysis inferred based on the complete genomes of the family Nodaviridae
Data in Brief, 2016 In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported.
Chen-Fei Low, Hamidun Bunawan
doaj
Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. [PDF]
Nucleic Acids Res, 2023 Zong F +6 more
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Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. [PDF]
Zool Res, 2023 Liu GM +16 more
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Phylogenetic automata, pruning, and multiple alignment [PDF]
arXiv, 2011 We present an extension of Felsenstein's algorithm to indel models defined on entire sequences, without the need to condition on one multiple alignment. The algorithm makes use of a generalization from probabilistic substitution matrices to weighted finite-state transducers.
arxiv
Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage. [PDF]
BMC Bioinformatics, 2023 Xie R, Zan X, Chu L, Su Y, Xu P, Liu W.
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Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families. [PDF]
NAR Genom Bioinform, 2022 Hubley R, Wheeler TJ, Smit AFA.
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Parallel DNA Sequence Alignment on High-Performance Systems with CUDA and MPI [PDF]
arXivSequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a robust and accurate method for global sequence alignment.
arxiv
Joint alignment of multiple protein-protein interaction networks via convex optimization [PDF]
arXiv, 2016 Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps identify conserved sub-networks and provides extra information for functional annotations.
arxiv
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. [PDF]
Bioinformatics, 2022 Shen C, Zaharias P, Warnow T.
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