The usage tables are created to facilitate examination
of the codon preference in various nematode species. The importance
of considering the variation in amino acid codon usage comes from
the degenerate nature of the genetic code. Most of the 20 amino
acids are encoded by more than one codon. Patterns of nucleotide
usage are of great importance in the definition and functional
investigation of coding regions. In addition, intra- and intercodon
variations may determine the extent of dissimilarity for divergent
but structurally and functionally conserved genes and influence
the outcome of phylogenetic analyses. Genes in an organism or
in related species generally show the same pattern of codon usage.
Comparisons within and between nematode clade members can reveal
the degree of pattern conservation and allow investigating of
whether the conservation is across all the members of the phylum
Nematoda or only members of a common phylogenetic order/family.
Furthermore, this information is valuable in the design of primers
for PCR and examination of exon boundaries.
The degree of preference of the four nucleotides C, G, A and U in the three positions I, II and III of the codons of partial coding sequences of various nematodes is examined. The nucleotide data (contig consensus sequences) examined were obtained by NemaGene clustering. Only complete triplets were considered. The EMBOSS tool 'cusp' ( http://biochem.dental.upenn.edu/EMBOSS-HELP/cusp.html) was used to calculate the amino acids and codon usage frequencies.