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Multiple sequence alignment accuracy and evolutionary distance estimation
BMC Bioinformatics, 2005 Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and ...
Rosenberg Michael S
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2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles [PDF]
, 2011 Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-
Hoi Shan Kwan +3 more
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MAFFT version 5: improvement in accuracy of multiple sequence alignment
Nucleic Acids Research, 2005 The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective ...
K. Katoh, K. Kuma, H. Toh, T. Miyata
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A Mutual Information Based Sequence Distance For Vertebrate Phylogeny Using Complete Mitochondrial Genomes [PDF]
, 2007 Traditional sequence distances require alignment. A new mutual information based sequence distance without alignment is defined in this paper. This distance is based on compositional vectors of DNA sequences or protein sequences from complete genomes ...
Anh, Vo +3 more
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Optimization of sequence alignment for simple sequence repeat regions
BMC Research Notes, 2011 Background Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome.
Ogbonnaya Francis C +2 more
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PLoS ONE, 2020 Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information for structural ...
Amir H Bayegan, Peter Clote
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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
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Local Alignment of DNA Sequence Based on Deep Reinforcement Learning
IEEE Open Journal of Engineering in Medicine and Biology, 2021 Goal: Over the decades, there have been improvements in the sequence alignment algorithm, with significant advances in various aspects such as complexity and accuracy. However, human-defined algorithms have an explicit limitation in view of developmental
Yong-Joon Song, Dong-Ho Cho
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Fair Evaluation of Global Network Aligners [PDF]
, 2014 Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in different ...
Crawford, Joseph +2 more
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SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
Bioinform., 2012 MOTIVATION In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly
E. Pruesse, J. Peplies, F. Glöckner
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