Related papers: Genome Compression Against a Reference
Successful sequencing experiments require judicious sample selection. However, this selection must often be performed on the basis of limited preliminary data. Predicting the statistical properties of the final sample based on preliminary…
This paper proposes a novel approach for storing and retrieving massive DNA sequences.. The method is based on a perceptual hash function, commonly used to determine the similarity between digital images, that we adapted for DNA sequences.…
The effects of inbreeding on human health depend critically on the number and severity of recessive, deleterious mutations carried by individuals. In humans, existing estimates of these quantities are based on comparisons between…
The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
The amount of non-unique sequence (non-singletons) in a genome directly affects the difficulty of read alignment to a reference assembly for high throughput-sequencing data. Although a greater length increases the chance for reads being…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
Very low levels of genetic diversity have been reported in vertebrates with large genomes, notably salamanders and lungfish [1-3]. Interpreting differences in heterozygosity, which reflects genetic diversity in a population, is complicated…
Background: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but generally do not scale to arbitrarily…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
How does the genome encode the form of the organism? What is the nature of this genomic code? Inspired by recent work in machine learning and neuroscience, we propose that the genome encodes a generative model of the organism. In this…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…