Related papers: Information Analysis of DNA Sequences
An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…
By means of the concept of Factorial Moments we examine DNA sequences from Yeast to distinguish coding and non-coding regions. It is found that the FM may be a powerful tool for analysis of DNA sequences. PACS numbers:…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
We introduce a complexity measure for symbolic sequences. Starting from a segmentation procedure of the sequence, we define its complexity as the entropy of the distribution of lengths of the domains of relatively uniform composition in…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
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…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
Background: Trace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
Quantification of information content and its temporal variation in intracellular calcium spike trains in neurons helps one understand functions such as memory, learning, and cognition. Such quantification could also reveal pathological…
The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the…
The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth…