相关论文: Simplified amino acid alphabets based on deviation…
New lower bounds on the minimum average Hamming distance of binary codes are derived. The bounds are obtained using linear programming approach.
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
Signal processing (SP) techniques convert DNA and protein sequences into information that lead to successful drug discovery. One must, however, be aware about the difference between information and entropy1. Eight other physical properties…
Of the twenty amino acids used in proteins, ten were formed in Miller's atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth…
We call \emph{Alphabet model} a generalization to N types of particles of the classic ABC model. We have particles of different types stochastically evolving on a one dimensional lattice with an exchange dynamics. The rates of exchange are…
There is a common problem of operating on hash values of elements of some database. In this paper there will be analyzed informational content of such general task and how to practically approach such found lower boundaries. Minimal prefix…
A binary word is Sturmian if the occurrences of each letter are balanced, in the sense that in any two factors of the same length, the difference between the number of occurrences of the same letter is at most 1. In digital geometry,…
In many applications of natural language processing (NLP) it is necessary to determine the likelihood of a given word combination. For example, a speech recognizer may need to determine which of the two word combinations ``eat a peach'' and…
We derive the amino acid assignment to one codon representation (typical 64-dimensional irreducible representation) of the basic classical Lie superalgebra osp(5|2) from biochemical arguments. We motivate the approach of mathematical…
We present and implement a distance-based clustering of amino acids within the framework of a statistically derived interaction matrix and show that the resulting groups faithfully reproduce, for well-designed sequences, thermodynamic…
We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method, the data is organized into a binary…
Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of…
Boolean tensor decomposition approximates data of multi-way binary relationships as product of interpretable low-rank binary factors, following the rules of Boolean algebra. Here, we present its first probabilistic treatment. We facilitate…
We consider the problem of sparse coding, where each sample consists of a sparse linear combination of a set of dictionary atoms, and the task is to learn both the dictionary elements and the mixing coefficients. Alternating minimization is…
This work aims at showing the relevance and the applications possibilities of the Fibonacci sequence, and also its q-deformed or quantum extension, in the study of the genetic code(s). First, after the presentation of a new formula, an…
In this paper it is shown that within a Combined Genetic Code Table, realized through a combination of Watson-Crick Table and Codon Path Cube it exists, without an exception, a strict distinction between two classes of enzymes…
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
We perform an exhaustive analysis of genome statistics for organisms, particularly extremophiles, growing in a wide range of physicochemical conditions. Specifically, we demonstrate how the correlation between the frequency of amino acids…
In nonadaptive group testing, the main research objective is to design an efficient algorithm to identify a set of up to $t$ positive elements among $n$ samples with as few tests as possible. Disjunct matrices and separable matrices are two…