Related papers: Comparative statistical analysis of bacteria genom…
The length of coding sequence series in microbial genomes were regarded as a fluctuating system and characterized by the methods of statistical physics. The distribution and the correlatin properties of 50 genomes including bacteria and…
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…
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…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…
Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been…
This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences.…
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…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
In our paper selected linguistic features of genomes to study the statistics of the gene codes are considered. We present the information theory from which it follows that if the system is described by distributions of hyperbolic type it…
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…
We define and completely solve a content-based directed network whose nodes consist of random words and an adjacency rule involving perfect or approximate matches, for an alphabet with an arbitrary number of letters. The analytic expression…
In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
We study statistical properties of DNA chains of thirteen microbial complete genomes. We find that the power spectrum of several of the sequences studied flattens off in the low frequency limit. This implies that the correlation length in…
Given a random text over a finite alphabet, we study the frequencies at which fixed-length words occur as subsequences. As the data size grows, the joint distribution of word counts exhibits a rich asymptotic structure. We investigate all…
Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively…
Previous investigation of coding sequence lengths (CDS) in the bacterial circular chromosome revealed short range correlation in the series of these data. We have further analyzed the averaged periodograms of these series and we found that…