CompoDynamics: a comprehensive database for characterizing sequence composition dynamics

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Sequence composition significantly influences gene expression, RNA stability, translation efficiency, and molecular function.
• Understanding these compositional dynamics is crucial for genome evolution and adaptation studies across all life forms.
• A centralized, comprehensive resource for sequence composition data is essential for diverse biological research.

Purpose of the Study:

• To introduce CompoDynamics, a novel database for comprehensive sequence composition analysis of coding sequences (CDSs) and genomes.
• To provide a rich repository of nucleotide content, codon usage, amino acid usage, and derived molecular features.
• To offer interactive tools for comparative analyses of sequence composition across species and gene groups.

Main Methods:

• Leveraged RefSeq data to curate a large-scale database.
• Collected sequence composition data including nucleotide content, codon usage, and amino acid usage.
• Integrated derived features such as coding potential, physicochemical properties, and phase separation propensity.

Main Results:

• CompoDynamics contains data for 118,689,747 high-quality CDSs and 34,562 genomes from 24,995 species.
• The database includes nucleotide content, codon usage, amino acid usage, coding potential, physicochemical properties, and phase separation data.
• Interactive tools facilitate comparative analysis of sequence composition and molecular features.

Conclusions:

• CompoDynamics provides a fundamental resource for studying sequence composition dynamics across genes and genomes.
• The database supports a broad spectrum of biological studies by offering extensive sequence composition data and analytical tools.
• Facilitates deeper understanding of the roles of sequence composition in biological processes and evolution.