Genome analysis with inter-nucleotide distances

Afreixo, Vera; Bastos, Carlos A. C.; Pinho, Armando J.; Garcia, Sara P.; Ferreira, Paulo J. S. G.

doi:10.1093/bioinformatics/btp546

Cited by 76 publications

(70 citation statements)

References 21 publications

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“…We also used the IN distance relative error used in (Afreixo et al, 2009) and we concatenated the first 100 IN distances and the first 20 ND distance relative errors. Only the first 20 ND distances were used, because for larger distances the distributions become sparse.…”

Section: Numerical Proceduresmentioning

confidence: 99%

“…However, several other different mappings have been proposed (see for example, Silverman and Linsker (1986); Jeffrey (1990); Zhang and Zhang (1994); Buldyrev et al (1995); Anastassiou (2001) In a previous work, we explored the inter-nucleotide (IN) distance, the distance to the first occurrence of the same symbol, to perform a comparative analysis between species (Afreixo et al, 2009). In this work, we present a new DNA numerical profile and a new mapping to explore the correlation structure of DNA: the distance to the nearest dissimilar (ND) nucleotide.…”

Section: Introductionmentioning

confidence: 99%

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Genome analysis with distance to the nearest dissimilar nucleotide

Afreixo

Bastos

Pinho

et al. 2011

Journal of Theoretical Biology

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DNA may be represented by sequences of four symbols, but it is often useful to convert those symbols into real or complex numbers for further analysis.Several mapping schemes have been used in the past, but most of them seem to be unrelated to any intrinsic characteristic of DNA. The objective of this work was to study a mapping scheme that is directly related to DNA characteristics, and that could be useful in discriminating between different species.Recently, we have proposed a methodology based on the inter-nucleotide distance, which proved to contribute to the discrimination among species. In this paper, we introduce a new distance, the distance to the nearest dissimilar nucleotide, which is the distance of a nucleotide to first occurrence of a different nucleotide. This distance is related to the repetition structure of single nucleotides. Using the information resulting from the concatenation of the distance to the nearest dissimilar and the inter-nucleotide distance, we found that this new distance brings additional discriminative capabilities. Preprint submitted to Journal of Theoretical BiologyJanuary 31, 2011 This suggests that the distance to the nearest dissimilar nucleotide might contribute with useful information about the evolution of the species.

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Section: Numerical Proceduresmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome analysis with distance to the nearest dissimilar nucleotide

Afreixo

Bastos

Pinho

et al. 2011

Journal of Theoretical Biology

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“…In a simple way, DNA sequences are non-numerical sequences of the four-letter alphabet, A, C, G and T , which stands for the four nucleotides: Adenine, Cytosine, Guanine, and Thymine. Various transformations of DNA sequences into numerical data have been proposed in order to take advantage of methodologies available for quantitative data ( [2,9,15,16,3,18,1]). Free-alignment algorithms have been applied to build distance trees aimed at visualizing historical evolutionary relationships among species (e.g., [21,23]).…”

Section: Introductionmentioning

confidence: 99%

“…Several numerical transformations of DNA sequences have been used to perform multiple organism comparisons. Basically, observed DNA sequences and randomly ordered sequences (random background) are compared using different procedures and discrepancy measures based either on genomic symbol frequencies (e.g., [22,14,13,20]) or on genomic symbol distance frequencies (e.g., [1]). This type of residual analysis can highlight the contribution of DNA selective evolution of each species ( [17]).…”

Section: Introductionmentioning

confidence: 99%

Mixture models of geometric distributions in genomic analysis of inter-nucleotide distances

Freitas

Afreixo

Escudeiro³

2013

Stat., optim. inf. comput.

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The mapping defined by inter-nucleotide distances (InD) provides a reversible numerical representation of the primary structure of DNA. If nucleotides were independently placed along the genome, a finite mixture model of four geometric distributions could be fitted to the InD where the four marginal distributions would be the expected distributions of the four nucleotide types. We analyze a finite mixture model of geometric distributions (f 2 ), with marginals not explicitly addressed to the nucleotide types, as an approximation to the InD. We use BIC in the composite likelihood framework for choosing the number of components of the mixture and the EM algorithm for estimating the model parameters. Based on divergence profiles, an experimental study was carried out on the complete genomes of 45 species to evaluate f 2 . Although the proposed model is not suited to the InD, our analysis shows that divergence profiles involving the empirical distribution of the InD are also exhibited by profiles involving f 2 . It suggests that statistical regularities of the InD can be described by the model f 2 . Some characteristics of the DNA sequences captured by the model f 2 are illustrated. In particular, clusterings of subgroups of eukaryotes (primates, mammalians, animals and plants) are detected.

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“…a study of correlation information, sequence periodicities, and other sequence characteristics. More examples of studies focused on statistical properties of DNA sequences and also on their biological interpretation may be found in [12,13].…”

Section: Introductionmentioning

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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Genome analysis with inter-nucleotide distances

Cited by 76 publications

References 21 publications

Genome analysis with distance to the nearest dissimilar nucleotide

Genome analysis with distance to the nearest dissimilar nucleotide

Mixture models of geometric distributions in genomic analysis of inter-nucleotide distances

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

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