Related papers: Mapping to a Reference Genome Structure
The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional…
How to define and use the concept of inclusive fitness is a contentious topic in evolutionary theory. Inclusive fitness can be used to calculate selection on a focal gene, but it is also applied to whole organisms. Individuals are then…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
We discuss a model of genome as a program with functional architecture and consider the approach to Darwinian evolution as a learning problem for functional programming. In particular we introduce a model of learning for some class of…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…
In this research, we consider a mixture of genome fragments of a certain bacteria set. The problem of mixture separation is studied under the assumption that all the genomes present in the mixture are completely sequenced or are close to…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…
Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about…
What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…