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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 ( 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 A simple PERL script was written to tally codon usage. Start codons and stop codons were not included in codon usage counts.

Todd M. Lowe