GenDecoder: genetic code prediction for metazoan mitochondria

Abstract

Although the majority of the organisms use the same genetic code to translate DNA, several variants have been described in a wide range of organisms, both in nuclear and organellar systems, many of them corresponding to metazoan mitochondria. These variants are usually found by comparative sequence analyses, either conducted manually or with the computer. Basically, when a particular codon in a query-species is linked to positions for which a specific amino acid is consistently found in other species, then that particular codon is expected to translate as that specific amino acid. Importantly, and despite the simplicity of this approach, there are no available tools to help predicting the genetic code of an organism. We present here GenDecoder, a web server for the characterization and prediction of mitochondrial genetic codes in animals. The analysis of automatic predictions for 681 metazoans aimed us to study some properties of the comparative method, in particular, the relationship among sequence conservation, taxonomic sampling and reliability of assignments. Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from http://darwin.uvigo.es/software/gendecoder.html.

Figure 1

Scheme of GenDecoder's workflow. The example is based on the UCU codon. A similar pipeline is executed for every other codon and using the whole set of 13 mitochondrial protein-coding genes.

Figure 2

Performance of GenDecoder under different entropy thresholds and using the sampling-balanced alignments. The accuracy under different parameters for 41 042 codon assignments corresponding to 681 species is summarized in the graph. In every case columns with >20% of gaps were ignored. Comparison of this figure with the one appearing in (3) indicates that the use of taxonomically balanced alignments displaces the optimal point towards less restrictive entropy thresholds.

Figure 3

GenDecoder output for the acantocephalan L.thecatus. Codon-imp, number of codons at conserved positions (in this case S < 2.0, gaps < 20%); Codon-num, number of codons in the mt-genome; Freq-aa, first decimal in the frequency of the most frequent amino acid; Diff-freq, difference between the frequency of the predicted and expected amino acids (first decimal).