Transfer RNAs in C. elegans were detected using the program tRNAscan-SE with the default (eukaryote-specific) parameters [Lowe & Eddy, 1997]. The C. elegans genome sequence was retrieved from the Genome Sequencing Center website (http://genome.wustl.edu/gsc/C_elegans/) on December 11, 1998. Probable pseudogenes were detected automatically by the program, and were visually inspected to classify the type of pseudogene.
Codon frequency counts were derived from Wormpep16, a manually reviewed collection of 16,328 predicted protein coding genes from C. elegans (available at ftp://ftp.sanger.ac.uk/pub/databases/wormpep/wormpep16cdnas.dna). A simple PERL script was written to tally codon usage. Start codons and stop codons were not included in codon usage counts.