Related papers: Simplified amino acid alphabets based on deviation…
We provide a new methodology for statistical recovery of single linear mixtures of piecewise constant signals (sources) with unknown mixing weights and change points in a multiscale fashion. We show exact recovery within an…
For a broad class of input-output maps, arguments based on the coding theorem from algorithmic information theory (AIT) predict that simple (low Kolmogorov complexity) outputs are exponentially more likely to occur upon uniform random…
Scientific documents often contain a large number of acronyms. Disambiguation of these acronyms will help researchers better understand the meaning of vocabulary in the documents. In the past, thanks to large amounts of data from English…
A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature…
For applications in concatenated coding for optical communications systems, we examine soft-demapping of short spherical codes constructed as constant-energy shells of the Cartesian power of pulse amplitude modulation constellations. These…
An alphabetic binary tree formulation applies to problems in which an outcome needs to be determined via alphabetically ordered search prior to the termination of some window of opportunity. Rather than finding a decision tree minimizing…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
A method is described where the aminoacyl-tRNA synthetase system is used to create very small devices for quantitative analysis of the amino acids that occur in proteins. The basis of the method is that each of the 20 synthetases and/or a…
Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…
Imposing a minimum principle in the framework of the so called crystal basis model of the genetic code, we determine the structure of the minimum set of 22 anticodons which allows the translational-transcription for animal mitochondrial…
Grammar-based compression is a popular and powerful approach to compressing repetitive texts but until recently its relatively poor time-space trade-offs during real-life construction made it impractical for truly massive datasets such as…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
In protein secondary structure prediction, each amino acid in sequence is typically treated as a distinct category and represented by a one-hot vector. In this study, we developed two novel chemical representations for amino acids utilizing…
The algebraic structures of the genetic code are most important to obtain additional information about the semantic code and its applications. In this paper we define two dual Boolean codon lattices of the genetic code using hydrogen bond…
We combine the standard 1992 20x20 substitution matrix based on block alignment, BLOSUM62, with the standard 1982 amino acid hydropathicity scale KD as well as the modern 2007 hydropathicity scale MZ, and compare the results. The…
If p is the probability of a letter of a memoryless source, the length l of the corresponding binary Huffman codeword can be very different from the value -log p. We show that, nevertheless, for a typical letter, l is approximately equal to…
Information theoretic analysis of genetic languages indicates that the naturally occurring 20 amino acids and the triplet genetic code arose by duplication of 10 amino acids of class-II and a doublet genetic code having codons NNY and…
The efficiency of a code is estimated by its redundancy $R$, while the complexity of a code is estimated by its average delay $\bar N$. In this work we construct word-based codes, for which $R \lesssim \bar N^{-5/3}$. Therefore, word-based…