A word recurrence based algorithm to extract genomic dictionaries

2020/09/22 by Vincenzo Bonnici, Bonnici, Vincenzo, Giuditta Franco +3
Biochemistry, Genetics and Molecular Biology · #FOS: Biological sciences #FOS: Computer and information sciences #Fractal and DNA sequence analysis #Genomics (q-bio.GN) #Genomics and Phylogenetic Studies #Information Theory (cs.IT) #RNA and protein synthesis mechanisms

paper · pdf · doi:10.48550/arxiv.2009.10449

openalex publication_date 2020/09/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is proposed, to extract significant (relatively small) dictionaries of genomic words. Namely, conceptual analyses are here combined with empirical studies, to open up a methodology for the extraction of variable length dictionaries from genomic sequences, based on the information content of some factors. Its application to human chromosomes highlights an original inter-chromosomal similarity in terms of factor distributions.

Citations

• The language of genes
• Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
• rm K-SVD: An Algorithm for Designing Overcomplete Dictionaries for Sparse Representation
• A Simplex Method for Function Minimization

Related

• Information Theory of Genomes
• Reconsidering the significance of genomic word frequency
• Information and order of genomic sequences within chromosomes as identified by complexity theory. An integrated methodology
• Identifying statistical dependence in genomic sequences via mutual information estimates
• Finding Structure in Text, Genome and Other Symbolic Sequences