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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
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Multiple alignment-free sequence comparison [PDF]
Bioinformatics, 2013 Abstract Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences.
Ren, J +4 more
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Sequence embedding for fast construction of guide trees for multiple sequence alignment
Algorithms for Molecular Biology, 2010 Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences.
Wilm Andreas +4 more
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A statistical score for assessing the quality of multiple sequence alignments
BMC Bioinformatics, 2006 Background Multiple sequence alignment is the foundation of many important applications in bioinformatics that aim at detecting functionally important regions, predicting protein structures, building phylogenetic trees etc.
Aittokallio Tero +3 more
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Progressive multiple sequence alignments from triplets [PDF]
BMC Bioinformatics, 2007 The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors ...
Kruspe, Matthias, Stadler, Peter F.
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SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation
BMC Bioinformatics, 2011 Background Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields.
Strope Cory L +2 more
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Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences [PDF]
Journal of Computational Biology, 2007 Despite considerable efforts, it remains difficult to obtain accurate multiple sequence alignments. By using additional hits from database search of the input sequences, a few strategies have been proposed to significantly improve alignment accuracy, including the construction of profiles from the hits while performing profile alignment, the inclusion ...
Yue, Lu, Sing-Hoi, Sze
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Molecules, 2018 Residues in proteins that are in close spatial proximity are more prone to covariate as their interactions are likely to be preserved due to structural and evolutionary constraints.
Patrice Koehl +2 more
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Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment
BMC Bioinformatics, 2012 Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains.
Daniels Noah M +2 more
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BMC Research Notes, 2012 Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs) and other related ...
Zuiter Afnan +2 more
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