NemaGene : codon usage tables

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CODON USAGE TABLES

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.  

Last Update: 08-31-2011
Amino acids and codon usage frequencies calculated using species' NemaGene
consensus sequences (Nematode.net)
Species
Consensus source
Codon Usage Table
Ancylostoma caninum
454 Newbler assembly
Ancylostoma ceylanicum
Sanger PCAP assembly
Brugia malayi
Sanger PCAP assembly
Cooperia oncophora
454 Newbler assembly
Globodera rostochiensis
Sanger PCAP assembly
Haemonchus contortus
Sanger PCAP assembly
Heterorhabditis bacteriophora
454 Newbler assembly
Meloidogyne chitwoodi
Sanger PCAP assembly
Meloidogyne hapla
Sanger PCAP assembly
Meloidogyne incognita
Sanger PCAP assembly
Necator americanus
454 Newbler assembly
Oesophagostomum dentatum
454 Newbler assembly
Ostertagia ostertagi
454 Newbler assembly
Pratylenchus penetrans
Sanger PCAP assembly
Strongyloides ratti
Sanger PCAP assembly
Strongyloides stercoralis
Sanger PCAP assembly
Trichinella spiralis
Sanger PCAP assembly
Trichuris vulpis
Sanger PCAP assembly
Teladorsagia circumcincta
454 Newbler assembly
Trichostrongylus colubriformis
454 Newbler assembly
 
Amino acids and codon usage frequencies calculated via methods described in the paper:
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species (Genome Biology 2006)
Species
Consensus source
Codon Usage Table
Ancylostoma caninum
Sanger PCAP assembly
Ancylostoma ceylanicum
Sanger PCAP assembly
Ascaris lumbricoides
Sanger PCAP assembly
Ascaris suum
Sanger PCAP assembly
Brugia malayi
Sanger PCAP assembly
Dirofilaria immitis
Sanger PCAP assembly
Globodera pallida
Sanger PCAP assembly
Globodera rostochiensis
Sanger PCAP assembly
Haemonchus contortus
Sanger PCAP assembly
Heterodera glycines
Sanger PCAP assembly
Meloidogyne arenaria
Sanger PCAP assembly
Meloidogyne chitwoodi
Sanger PCAP assembly
Meloidogyne hapla
Sanger PCAP assembly
Meloidogyne incognita
Sanger PCAP assembly
Meloidogyne javanica
Sanger PCAP assembly
Necator americanus
Sanger PCAP assembly
Nippostrongylus brasiliensis
Sanger PCAP assembly
Ostertagia ostertagi
Sanger PCAP assembly
Onchocerca volvulus
Sanger PCAP assembly
Pratylenchus penetrans
Sanger PCAP assembly
Pristionchus pacificus
Sanger PCAP assembly
Parastrongyloides trichosuri
Sanger PCAP assembly
Strongyloides ratti
Sanger PCAP assembly
Strongyloides stercoralis
Sanger PCAP assembly
Trichostrongylus colubriformis
Sanger PCAP assembly
Teladorsagia circumcincta
Sanger PCAP assembly
Trichuris muris
Sanger PCAP assembly
Trichinella spiralis
Sanger PCAP assembly
Trichuris vulpis
Sanger PCAP assembly
Zeldia punctata
Sanger PCAP assembly

 
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