相关论文: The genetic code multiplet structure, in one numbe…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
The biological distinction between the base positions in the codon, the chemical types of bases (purine and pyrimidine) and their hydrogen bond number have been the most relevant codon properties used in the genetic code analysis. Now,…
It is shown that there is a sense in splitting Genetic Code Table (GCT) into three parts using the harmonic mean, calculated by the formula H (a, b) = 2ab / (a + b), where a = 63 and b = 31.5. Within these three parts, the amino acids (AAs)…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
We show how good quantum error-correcting codes can be constructed using generalized concatenation. The inner codes are quantum codes, the outer codes can be linear or nonlinear classical codes. Many new good codes are found, including both…
The subject of pattern avoiding permutations has its roots in computer science, namely in the problem of sorting a permutation through a stack. A formula for the number of permutations of length n that can be sorted by passing it twice…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
The classical derangement numbers count fixed point-free permutations. In this paper we study the enumeration problem of generalized derangements, when some of the elements are restricted to be in distinct cycles in the cycle decomposition.…
A composition of a nonnegative integer (n) is a sequence of positive integers whose sum is (n). A composition is palindromic if it is unchanged when its terms are read in reverse order. We provide a generating function for the number of…
Unimodal (i.e. single-humped) permutations may be decomposed into a product of disjoint cycles. Some enumerative results concerning their cyclic structure -- e.g. 2/3 of them contain fixed points -- are given. We also obtain in effect a…
We consider a general concept of composition and decomposition of objects, and discuss a few natural properties one may expect from a reasonable choice thereof. It will be demonstrated how this leads to multiplication and co- multiplication…
We define the operation of composing two hereditary classes of permutations using the standard composition of permutations as functions and we explore properties and structure of permutation classes considering this operation. We mostly…
Motivated by charge balancing constraints for rank modulation schemes, we introduce the notion of balanced permutations and derive the capacity of balanced permutation codes. We also describe simple interleaving methods for permutation code…
The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the…
In this paper, we introduce a new way of constructing and decoding multipermutation codes. Multipermutations are permutations of a multiset that may consist of duplicate entries. We first introduce a new class of matrices called…
In a prime number decomposition of integers in a given set, the occurrence frequencies of prime numbers are shown to satisfy a general forms of Zipf's law.
A primitive $k$-batch code encodes a string $x$ of length $n$ into string $y$ of length $N$, such that each multiset of $k$ symbols from $x$ has $k$ mutually disjoint recovering sets from $y$. We develop new explicit and random coding…
We enumerate permutations in the two permutation classes $\text{Av}_n(312, 4321)$ and $\text{Av}_n(321, 4123)$ by the number of cycles each permutation admits. We also refine this enumeration with respect to several statistics.
A permutation may be represented by a collection of paths in the plane. We consider a natural class of such representations, which we call tangles, in which the paths consist of straight segments at 45 degree angles, and the permutation is…
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.…