Related papers: Comparing reverse complementary genomic words base…
Probabilistic context-free grammars (PCFGs) are used to define distributions over strings, and are powerful modelling tools in a number of areas, including natural language processing, software engineering, model checking, bio-informatics,…
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…
Background: Zipf's discovery that word frequency distributions obey a power law established parallels between biological and physical processes, and language, laying the groundwork for a complex systems perspective on human communication.…
Understanding epistasis (genetic interaction) may shed some light on the genomic basis of common diseases, including disorders of maximum interest due to their high socioeconomic burden, like schizophrenia. Distance correlation is an…
Statistical analysis of bacteria genomes texts has been performed on the basis of 20 complete genomes origin from Genebank. It has been revealed that the word ranked distributions are quite well approximated by logarithmic law. Results…
A new family of compound Poisson distribution functions from statistical linguistic is used to study the n-tuples and nucleotide composition features of DNA sequences. The relative frequency distribution of the 6-tuples and 7- tuples…
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…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
Discrepancy measures between probability distributions are at the core of statistical inference and machine learning. In many applications, distributions of interest are supported on different spaces, and yet a meaningful correspondence…
Long-range correlations are found in symbolic sequences from human language, music and DNA. Determining the span of correlations in dolphin whistle sequences is crucial for shedding light on their communicative complexity. Dolphin whistles…
The analysis of strings of $n$ random variables with geometric distribution has recently attracted renewed interest: Archibald et al. consider the number of distinct adjacent pairs in geometrically distributed words. They obtain the…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
Distance correlation has become an increasingly popular tool for detecting the nonlinear dependence between a pair of potentially high-dimensional random vectors. Most existing works have explored its asymptotic distributions under the null…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
Chargaff's second parity rule (CSPR) asserts that the frequencies of short polynucleotide chains are the same as those of the complementary reversed chains. Up to now, this hypothesis has only been observed empirically and there is…
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…
The Universal Similarity Metric (USM) has been demonstrated to give practically useful measures of "similarity" between sequence data. Here we have used the USM as an alternative distance metric in a K-Nearest Neighbours (K-NN) learner to…
Recent research has shown that static word embeddings can encode word frequency information. However, little has been studied about this phenomenon and its effects on downstream tasks. In the present work, we systematically study the…
Computing the similarity between two probability distributions is a recurring theme across control. We introduce a unified family of distances between the probability distributions of two random variables that is based on the discrepancy…