Related papers: Statistical linguistic study of DNA sequences
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
A family of consistent tests, derived from a characterization of the probability generating function, is proposed for assessing Poissonity against a wide class of count distributions, which includes some of the most frequently adopted…
Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…
This paper presents a novel method to segment/decode DNA sequences based on n-grams statistical language model. Firstly, we find the length of most DNA 'words' is 12 to 15 bps by analyzing the genomes of 12 model species. Then we design an…
In this article, we investigate the properties of phoneme N-grams across half of the world's languages. We investigate if the sizes of three different N-gram distributions of the world's language families obey a power law. Further, the…
The statistical methods derived and described in this thesis provide new ways to elucidate the structural properties of text and other symbolic sequences. Generically, these methods allow detection of a difference in the frequency of a…
The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
A fundamental characteristic of natural language is the high rate at which speakers produce novel expressions. Because of this novelty, a heavy-tail of rare events accounts for a significant amount of the total probability mass of…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Background: We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce…
The distributions of the number of occurrences of words (the distributions of words for short) play key roles in information theory, statistics, probability theory, ergodic theory, computer science, and DNA analysis. Bassino et al. 2010 and…
We examine the problem of family size statistics (the number of individuals carrying the same surname, or the same DNA sequence) in a given size subsample of an exponentially growing population. We approach the problem from two directions.…
Recent observations in the theory of verse and empirical metrics have suggested that constructing a verse line involves a pattern-matching search through a source text, and that the number of found elements (complete words totaling a…
We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found across all known genomes. Such a distribution…
A new generalization of the family of Poisson-G is called beta Poisson-G family of distribution. Useful expansions of the probability density function and the cumulative distribution function of the proposed family are derived and seen as…
In this article we survey properties of mixed Poisson distributions and probabilistic aspects of the Stirling transform: given a non-negative random variable $X$ with moment sequence $(\mu_s)_{s\in\mathbb{N}}$ we determine a discrete random…
Using recent results on the occurrence times of a string of symbols in a stochastic process with mixing properties, we present a new method for the search of rare words in biological sequences generally modelled by a Markov chain. We obtain…