Genomics | Bioinformatics | Evolutionary/Comparative Genetics
FACIL: Fast and accurate genetic code inference and logo
BE Dutilh*, R Jurgelenaite, R Szklarczyk, SAFT van Hijum, HR Harhangi, M Schmid, B de Wild, K-J Françoijs, HG Stunnenberg, M Strous, MSM Jetten, HJM Op den Camp, MA Huynen
*Corresponding author: BE Dutilh
Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
F1000 Posters 2011, 2: 1134 (poster) [ENGLISH]
Poster [3.89 MB] | Resulting articles
Presented at
San Diego Microbiology Group meeting 2011,
14 May 2011, 22
The intensification of environmental 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.
We introduce FACIL, 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.
The foraminifer Globobulimina pseudospinescens does not have any sequenced close relatives in the databases, yet we infer its alternative genetic code with high confidence values. Results are intuitively visualized in a Genetic Code Logo.
No relevant conflicts of interest declared.
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