FACIL: Fast and Accurate Genetic Code Inference and Logo

Dutilh, B. E.; Jurgelenaite, R.; Szklarczyk, R.; van Hijum, S. A. F. T.; Harhangi, H. R.; Schmid, M.; de Wild, B.; Françoijs, K. J.; Stunnenberg, H. G.; Strous, M.; Jetten, M. S. M.; Op den Camp, H. J. M.; Huynen, M. A.

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FACIL: Fast and Accurate Genetic Code Inference and Logo

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Strous, M.
Microbial Fitness Group, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Citation

Dutilh, B. E., Jurgelenaite, R., Szklarczyk, R., van Hijum, S. A. F. T., Harhangi, H. R., Schmid, M., et al. (2011). FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics, 27(14), 1929-1933.

Cite as: https://hdl.handle.net/21.11116/0000-0001-C941-3

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.