FACIL: Fast and Accurate Genetic Code Inference and Logo

Abstract

Motivation: The intensification of DNA sequencing will increasingly unveil uncharacterized species with potential alternative genetic codes. A total of 0.65% of the DNA sequences currently in Genbank encode their proteins with a variant genetic code, and these exceptions occur in many unrelated taxa.

Results: We introduce FACIL (Fast and Accurate genetic Code Inference and Logo), a fast and reliable tool to evaluate nucleic acid sequences for their genetic code that detects alternative codes even in species distantly related to known organisms. To illustrate this, we apply FACIL to a set of mitochondrial genomic contigs of Globobulimina pseudospinescens. This foraminifer does not have any sequenced close relative in the databases, yet we infer its alternative genetic code with high confidence values. Results are intuitively visualized in a Genetic Code Logo.

Availability and implementation: FACIL is available as a web-based service at http://www.cmbi.ru.nl/FACIL/ and as a stand-alone program.

Fig. 1.

Outline of the FACIL algorithm, see text for details. The Genetic Code Logo visualizes the results, including the reliability of alternative genetic code predictions. The example shows the predicted code for G.pseudospinescens mitochondrial fragments, generated by entering the ‘example’ input data on the FACIL web server. The logo shows the 64 codons from left to right (predicted alternatives in red), each with a stack of AAs. The stack height indicates the percentage of RF3 trees supporting the predicted translation, the letter sizes indicate the scaled AA alignment scores and the red line is the percentage of RF1 or RF2 trees that predict a stop codon.

Fig. 2.

F₁-score for predicting coding (AA) and stop codons by homology alone and after RF filtering. Values are based on the predictions for all codons from the random fragments of bacterial, archaeal and organellar genomes (see Supplementary Table 2).