We determined various forces involved in shaping codon usage of the genes linked to brain
iron accumulation and
infantile neuroaxonal dystrophy. The analysis paved the way for determining the forces responsible for composition, expression level, physical properties and codon bias of a gene. An interesting observation related to composition was that, on all the three
codon positions, any two of the four
nucleotides had similar compositions. CpG, TpA, and GpT dinucleotides were underrepresented with the overrepresentation of TpG dinucleotide. CpG and TpA containing
codons ATA, CTA, TCG, and GCG were underrepresented, while TpG dinucleotide containing
codon CTG was overrepresented, indicative of compositional constraints importance. GC ending
codons were favored when the genome is GC rich, except
leucine encoding
codon TTG, which exhibits an inverse relationship with GC content.
Nucleotide disproportions are found associated with the physical properties of
proteins. The values of CAI and ENc are suggestive of low codon bias in genes. Considering the results of neutrality analysis, parity analysis, underrepresentation of TpA and CpG
codons, and over-representation of TpG
codons, the correlation between the compositional constraints and skew relationships with
protein properties suggested the role of all the three selectional, mutational and compositional forces in shaping codon usage with the dominance of selectional pressure.