Codon utilization, DNA landscaping and fractal analysis in bacteriophage phi(adh)

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Bacteriophage phi(adh) possesses a low G+C content genome.
• The phage utilizes a limited set of codons for protein synthesis.
• Understanding codon usage and nucleotide distribution is crucial for phage biology.

Purpose of the Study:

• To investigate the restricted codon usage in bacteriophage phi(adh).
• To analyze the distribution of purines and pyrimidines across the genome.
• To determine nucleotide positional bias within the phage genome and its ORFs.

Main Methods:

• Codon indices and distances were calculated for genes and ORFs.
• Purine and pyrimidine distribution was assessed on both DNA strands.
• Fractal analysis was employed to examine nucleotide positional bias.

Main Results:

• Codon distance analysis clustered genes and ORFs into four distinct groups.
• The plus strand showed higher purine content than the negative strand.
• ORFs exhibited a bias towards purines on the coding strand; fractal analysis indicated compositional bias over positional bias.

Conclusions:

• Bacteriophage phi(adh) displays non-random codon usage and nucleotide distribution.
• Strand-specific biases and purine enrichment on coding strands likely influence gene expression.
• The genome's nucleotide composition is characterized by self-similarity rather than positional bias.