New 3D graphical representation of DNA sequence based on dual nucleotides

Qi, Xiao-Qin; Wen, Jie; Zhang, Qi

doi:10.1016/j.jtbi.2007.08.025

Cited by 90 publications

(49 citation statements)

References 33 publications

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“…has independently analyzed cellular amino acid composition of bacteria, archaea, and eukaryotes (Sorimachi, 1999). Graphical representations and diagrammatic approaches to the study of complicated biological systems can provide intuitive pictures and useful insights (Chou, 1990;Qi X. Q., Won, & Qi Z. H., 2007). With the aid of certain graphical representations, simple patterns representing complicated organisms can be easily discerned from huge genomic data sets.…”

Section: Introductionmentioning

confidence: 99%

Classification of Non-Animals and Invertebrates Based on Amino Acid Composition of Complete Mitochondrial Genomes

Sorimachi¹,

Okayasu²

2013

IJB

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Amino acid compositions were predicted from data sets of 47 non-animal and 58 invertebrate animal complete mitochondrial genomes, which were chosen alphabetically based on scientific names without considering biological characteristics. Using Ward's clustering method with amino acid composition or nucleotide content as traits, non-animals were classified into Plantae, Chromalveolata, and Fungi, and invertebrates were classified into Animalia and primitive groups, Amoebozoa, Excavata, Protista, and Choanozoa. A combined sample set of primitive eukaryotes was also examined by cluster analysis using amino acid composition and nucleotide content. Some Amoebozoa comprised a single cluster, whereas other Amoebozoa were grouped with other organisms (Excavata, Prosista, Chromaleolata, Fungi and Plantae), indicating their close relationships. Choanozoa (choanoflagellates; Monosiga brevicollis), considered the closest living relatives of animals, were found to be instead closely related to Fungi (Smittium culisetae, Pleurotus ostreatus, and Epidermophyton floccosum) and Excavata (Malawimonas jakobiformis). Our results demonstrate that amino acid composition and nucleotide content are useful indices for characterizing non-animal and invertebrate complete mitochondrial genomes.

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Section: Introductionmentioning

confidence: 99%

Classification of Non-Animals and Invertebrates Based on Amino Acid Composition of Complete Mitochondrial Genomes

Sorimachi¹,

Okayasu²

2013

IJB

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“…Moreover, compared with others' work [1]- [5], [8]- [14], [19]- [28], our graphical curves are compact, that's to say, our graphical curves do not take up much room, and the complexities of computation is very small. Furthermore, the examination of similarities among the full coding sequences of globin gene of different species (see Table I) which were studied by Li et al [15] and Guo et al [29] and Li et al [30] and Qi et al [31] and Huang et al [32] and Guo et al [33] and Qi et al [34] shows our graphical representation method is more effective to the comparative study of DNA sequences.…”

Section: Introductionmentioning

confidence: 94%

Similarity/Dissimilarity of DNA Sequences Based on a New Condensed Curve Representation

Xiao¹

2014

IJMLC

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“…3D graphical representation of one sequence by four characteristic curves based on dinucletides has been proposed by Cao et al [130]. Other 3D graphical representations based on dinucleotides (PN-curves) [131], (DN-curves) [132], (D-curves) [133], or based on trinucleotides (TN-curves) [134] have been also proposed.…”

Section: Graphical Representations Of Dna Sequencesmentioning

confidence: 99%

Graphical and numerical representations of DNA sequences: statistical aspects of similarity

Bielińska-Wąż¹

2011

J Math Chem

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New approaches aiming at a detailed similarity/dissimilarity analysis of DNA sequences are formulated. Several corrections that enrich the information which may be derived from the alignment methods are proposed. The corrections take into account the distributions along the sequences of the aligned bases (neglected in the standard alignment methods). As a consequence, different aspects of similarity, as for example asymmetry of the gene structure, may be studied either using new similarity measures associated with four-component spectral representation of the DNA sequences or using alignment methods with corrections introduced in this paper. The corrections to the alignment methods and the statistical distribution moment-based descriptors derived from the four-component spectral representation of the DNA sequences are applied to similarity/dissimilarity studies of β-globin gene across species. The studies are supplemented by detailed similarity studies for histones H1 and H4 coding sequences. The data are described according to the latest version of the EMBL database. The work is supplemented by a concise review of the state-of-art graphical representations of DNA sequences.

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New 3D graphical representation of DNA sequence based on dual nucleotides

Cited by 90 publications

References 33 publications

Classification of Non-Animals and Invertebrates Based on Amino Acid Composition of Complete Mitochondrial Genomes

Classification of Non-Animals and Invertebrates Based on Amino Acid Composition of Complete Mitochondrial Genomes

Similarity/Dissimilarity of DNA Sequences Based on a New Condensed Curve Representation

Graphical and numerical representations of DNA sequences: statistical aspects of similarity

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