Structural and functional relationships shown by genomic analysis of Capra hircus genes

Abstract

The effect of base composition biases on codon usage patterns was investigated in the goat species Capra hircus, using custom-designed computational tools available within the public domain. Nucleotide frequencies were nearly equal and a slight increase of adenine–thymine (AT) over guanine–cytosine (GC) was detected throughout the dataset. However, this increase showed no influence on the bases at the third codon position (N3). C3 and G3 were found more often than A/T3, suggesting that there was a small or almost no influence of the general base composition on the N3 base composition. To understand more and analyse in-depth influence and interactions between base compositions and codons, further relative synonymous codon usage (RSCU) was investigated. Amino acid usage and the correlation between its usages were also investigated, using both basic sequence analysis and statistical analysis means (measures of correlation). These analyses were utilized to probe whether there were correlations between genes, genomic characteristics and their function. Genes with high GC and those with low GC were also investigated to see to what extent how a gene functions could influence its sequence structure and impose certain structural modifications. This investigation may shed light on many genomic features of Capra hircus genes and would be of significance for future biotechnology/research projects considering Capra for transgenic and advanced genomic initiatives.