Fractal and DNA sequence analysis

DNA nullomers as a statistical phenomenon

The paper shows that nullomers in genomes arise from statistical properties rather than evolutionary pressures or lethal effects.

UniWave-2: A Hybrid Model for Nucleic Acid Waveform Feature Extraction Enhanced by Fourier and Wavelet Transforms

UniWave-2 improves nucleic acid sequence analysis by integrating hydrophobicity, enhancing waveform resolution with Fourier and wavelet transforms, and using a lightweight GRU model for efficient feature extraction.

Genome-wide mapping of persistent long-range correlation in the complete telomere-to-telomere human reference genome

The paper maps long-range correlations in the complete telomere-to-telomere human genome, revealing heterogeneous genomic structure and chromosome-specific scaling.

Entropy Fusion DNA: Alignment-Free Gene Fusion Detection through Entropy and Mutual Information Descriptors

This paper introduces an alignment-free method using information-theoretic features to detect gene fusions, achieving strong performance in classification and partner prediction.

In silico restriction site analysis of whole genome sequences shows patterns caused by selection and sequence duplications

The paper analyzes whole genome sequences to identify non-random patterns in restriction site distributions, showing deviations from random sequences and effects of GC content and repetitive elements.

A deterministic computational kernel encoded in the human genome

The paper demonstrates that the human genome encodes a deterministic computational kernel with four properties, validated through analysis of proteome and chromosome data.

Quaternion Spectral Fingerprinting of DNA: GPU-Accelerated Multi-Channel Fourier Analysis for Alignment-Free Genomics

This paper introduces a quaternion Fourier transform framework for DNA sequence analysis, demonstrating its ability to detect structural periodicities and spectral signatures across multiple species.

Proteins as Statistical Languages: Information-Theoretic Signatures of Proteomes Across the Tree of Life

The paper introduces information-theoretic descriptors to analyze protein sequences as statistical languages, showing that real proteomes exhibit structured dependencies beyond simple compositional models.

dna-parser: a Python library written in Rust for fast encoding of DNA and RNA sequences

dna-parser encodes DNA and RNA sequences into numerical features efficiently using Rust and Python, offering fast and parallel processing.

UniWave: A Waveform-Based Encoding Framework for Nucleic Acid Feature Extraction

UniWave converts nucleotide sequences into continuous waveforms for improved genomic analysis, outperforming traditional methods in multiple tasks.

Efficient training of neural networks using natural vectors with covariates for the plant microRNA precursor prediction.

This study evaluates neural networks trained with natural vectors incorporating covariance for predicting plant microRNA precursors, showing improved performance in feature prediction and classification.

High dimensional tissue specific regulatory codes embedded in viral coding regions

This study shows that high dimensional silent patterns in viral coding regions encode regulatory codes related to viral tropism using a novel computational measure.

Discovery of Inverted Repeats and Palindromes in Viral Genomes

The paper identifies over 19 million inverted repeats in 14,000 viral genomes using BLMT, highlighting their prevalence and potential biological significance.

A DNA Sequence Imaging Approach to Predict Splice Sites Using Deep Learning

This paper introduces a DNA sequence imaging method for splice site prediction, showing that DFCP outperforms FCGR using deep learning on Arabidopsis and human data.

Frequency Chaos Game Representation - Singular Value Decomposition for Alignment-Free Phylogenetic Analysis

This paper introduces SVD-FCGR, an alignment-free phylogenetic analysis method using SVD on FCGR, showing improved resolution and scalability over MEGA for viral datasets.

Musical Insights into Protein Sequences and Functions via NMR Data

This paper converts protein sequences into music using NMR data, assigning notes based on amino acid frequencies and relaxation periods, and applies set theory to analyze homologous beta-globin sequences.

TIPs-VF: An augmented vector-based representation for variable-length DNA fragments with sequence, length, and positional awareness

TIPs-VF provides a variable-length DNA sequence encoding framework that improves representation of genetic sequences for machine learning by incorporating sequence, length, and positional awareness.

Prioritization of Lung Cancer Candidate Genes using Moment of Inertia Tensor Analysis

This study prioritizes lung cancer candidate genes using moment of inertia tensor analysis of amino acid physicochemical properties, identifying four genes linked to poor survival.

Improved Python Package for DNA Sequence Encoding using Frequency Chaos Game Representation

The paper introduces a Python package for DNA sequence encoding using Frequency Chaos Game Representation (FCGR), showing improved accuracy and efficiency over an R-based library for DNA sequences.

Complexity And Ergodicity In Chaos Game Representation Of Genomic Sequences

The paper analyzes the Chaos Game Representation of genomic sequences to assess ergodicity and finds that CGRs are non-ergodic due to distribution properties of nucleotide sequences.

Development of a fast feature extraction method for SARS-CoV-2 spike sequences using amino acid physicochemical properties

This paper develops a fast feature extraction method for SARS-CoV-2 spike sequences using amino acid physicochemical properties, achieving accurate clustering with reduced runtime compared to conventional methods.

Analysis of Sequences of Bases of Human DNA Using the Square Wave Method (SWM)

The paper describes the application of the Square Wave Method to analyze human DNA sequences and presents preliminary data supporting its potential functional relevance.

In-Silico analysis of Human Insulin Gene for Mirror repeat sequences

The paper identifies 210 mirror repeat sequences in the human insulin gene using an in silico approach called FPCB.

ortho_seqs: A Python tool for sequence analysis and higher order sequence-phenotype mapping

ortho_seqs quantifies sequence-phenotype interactions using tensor-based orthogonal polynomials, demonstrating its application to synthetic antibody sequences and other datasets.

Sequence-based Optimized Chaos Game Representation and Deep Learning for Peptide/Protein Classification

The paper develops a sequence-based chaos game representation combined with deep learning for peptide/protein classification, showing superior performance in hemolytic/non-hemolytic peptide and HIV protease mutant classification.

The Geometry of ATG-Walks of the Omicron SARS CoV-2 Virus RNAs

The paper analyzes ATG-walks of Omicron SARS-CoV-2 RNA sequences to compare their statistical characteristics with a reference RNA, finding small deviations and resistance to forming a new virus family.

Nfeature: A platform for computing features of nucleotide sequences

Nfeature computes a large number of features for DNA and RNA sequences, providing a standalone package and web platform for researchers.

Deep learning based on stacked sparse autoencoder applied to viral genome classification of SARS-CoV-2 virus

This paper applies stacked sparse autoencoders to classify SARS-CoV-2 genomes using k-mer image representations, achieving good performance in taxonomic classification.

DiviSSR: Simple arithmetic for efficient identification of tandem repeats

DiviSSR uses a mathematical property of 2-bit DNA representations to quickly and accurately identify tandem repeats in genomic data.

GBRAP: a tool to retrieve, parse and analyze GenBank files of viral and bacterial species

GBRAP is a Python tool that downloads, parses, and analyzes GenBank files for viral and bacterial genomes, providing various entropy and compositional analyses.