Related papers: An Alternative Cracking of The Genetic Code
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Living organisms are not just random collections of organic molecules. There is continuous information processing going on in the apparent bouncing around of molecules of life. Optimisation criteria in this information processing can be…
An open question asks if every knot of 4-genus g_s can be changed into a slice knot by g_s crossing changes. A counterexample is given.
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
In this paper we present a novel genetic algorithm (GA) solution to a simple yet challenging commercial puzzle game known as the Zen Puzzle Garden (ZPG). We describe the game in detail, before presenting a suitable encoding scheme and…
A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick…
Requiring stability of genetic code against translation errors, modelised by suitable mathematical operators in the crystal basis model of the genetic code, the main features of the organisation in multiplets of the mitochondrial and of the…
Algebraic properties of the genetic code are analyzed. The investigations of the genetic code on the basis of matrix approaches ("matrix genetics") are described. The degeneracy of the vertebrate mitochondria genetic code is reflected in…
Cartesian Genetic Programming is often used with a point mutation as the sole genetic operator. In this paper, we propose two phenotypic mutation techniques and take a step towards advanced phenotypic mutations in Cartesian Genetic…
Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961,…
We perform geometrization of genetics by representing genetic information by points of the 4-adic {\it information space.} By well known theorem of number theory this space can also be represented as the 2-adic space. The process of…
Answer Set Programming (ASP) is a powerful modeling formalism for combinatorial problems. However, writing ASP models is not trivial. We propose a novel method, called Sketched Answer Set Programming (SkASP), aiming at supporting the user…
Each of the individual factors of the Drake Equation is considered. Each in turn is either abandoned or redefined and finally reduced to a single new factor, fd, the fraction of technological life that is detectable by any means. However,…
In this paper we study the structure of specific linear codes called DNA codes. The first attempts on studying such codes have been proposed over four element rings which are naturally matched with DNA four letters. Later, double (pair) DNA…
We present an algorithm to compute the number of solutions of the (constrained) number partitioning problem. A concrete implementation of the algorithm on an Ising-type quantum computer is given.
The application of genetic algorithms (GAs) to many optimization problems in organizations often results in good performance and high quality solutions. For successful and efficient use of GAs, it is not enough to simply apply simple GAs…
We wish to minimize the resources used for network coding while achieving the desired throughput in a multicast scenario. We employ evolutionary approaches, based on a genetic algorithm, that avoid the computational complexity that makes…
It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the…