Related papers: Comparative statistical analysis of bacteria genom…
The field of computational linguistics constantly presents new challenges and topics for research. Whether it be analyzing word usage changes over time or identifying relationships between pairs of seemingly unrelated words. To this point,…
Statistical studies of languages have focused on the rank-frequency distribution of words. Instead, we introduce here a measure of how word ranks change in time and call this distribution \emph{rank diversity}. We calculate this diversity…
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…
Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
This study focuses on an alignment-free sequence comparison method: the number of words of length k shared between two sequences, also known as the D_2 statistic. The advantages of the use of this statistic over alignment-based methods are…
The distribution of bases spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution…
The genetic selection of keywords set, the text frequencies of which are considered as attributes in text classification analysis, has been analyzed. The genetic optimization was performed on a set of words, which is the fraction of the…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
Words are fundamental linguistic units that connect thoughts and things through meaning. However, words do not appear independently in a text sequence. The existence of syntactic rules induces correlations among neighboring words. Using an…
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…
This work proposes a markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and group…
The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling…
The recent dramatic increase in online data availability has allowed researchers to explore human culture with unprecedented detail, such as the growth and diversification of language. In particular, it provides statistical tools to explore…
The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two…
As is the case of many signals produced by complex systems, language presents a statistical structure that is balanced between order and disorder. Here we review and extend recent results from quantitative characterisations of the degree of…
Shaped by natural selection and other evolutionary forces, an organism's evolutionary history is reflected through its genome sequence, content of functional elements and organization. Consequently, organisms connected through phylogeny,…
In a recent Physical Review Letter, Mantegna et. al., report that certain statistical signatures of natural language can be found in non-coding DNA sequences. In this comment we show that random noise with power-law correlation similar to…
Our results demonstrated that a previously reported protein name co-occurrence method (5-mention PubGene) which was not based on a hypothesis testing framework, it is generally statistically more significant than the 99th percentile of…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…