FACIL: Fast and accurate genetic code inference and logo

Bas E. Dutilh; Rasa Jurgelenaite; Radek Szklarczyk; Sacha A.F.T. van Hijum; Harry R. Harhangi; Markus Schmid; Bart de Wild; Kees Jan Françoijs; Hendrik G. Stunnenberg; Marc Strous; Mike S.M. Jetten; Huub J.M. Op den Camp; Martijn A. Huynen

doi:10.1093/bioinformatics/btr316

FACIL: Fast and accurate genetic code inference and logo

Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A.F.T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees Jan Françoijs, Hendrik G. Stunnenberg, Marc Strous, Mike S.M. Jetten, Huub J.M. Op den Camp, Martijn A. Huynen

Research output: Contribution to journal › Article › peer-review

34 Citations (Scopus)

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.

Original language	English
Article number	btr316
Pages (from-to)	1929-1933
Number of pages	5
Journal	Bioinformatics
Volume	27
Issue number	14
DOIs	https://doi.org/10.1093/bioinformatics/btr316
Publication status	Published - Jul 2011
Externally published	Yes

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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. (2011). FACIL: Fast and accurate genetic code inference and logo. Bioinformatics, 27(14), 1929-1933. Article btr316. https://doi.org/10.1093/bioinformatics/btr316

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title = "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.",

author = "Dutilh, {Bas E.} and Rasa Jurgelenaite and Radek Szklarczyk and {van Hijum}, {Sacha A.F.T.} and Harhangi, {Harry R.} and Markus Schmid and {de Wild}, Bart and Fran{\c c}oijs, {Kees Jan} and Stunnenberg, {Hendrik G.} and Marc Strous and Jetten, {Mike S.M.} and {Op den Camp}, {Huub J.M.} and Huynen, {Martijn A.}",

note = "Funding Information: Funding: B.E.D. was supported by the Netherlands Organisation for Scientific Research (NWO) Horizon grant (050-71-058) and by NWO Veni grant (016.111.075). R.J. was supported through the Virgo consortium (BSIK 03012), an Innovative Cluster approved by the Netherlands Genomics Initiative. R.S. was supported by NWO Horizon grant (050-71-053). M.Sc. was supported by the Darwin Center for Biogeosciences (project 142.16.1091). M.St. was supported by European Research Council starting grant MASEM (242635). This work is part of the programme of BiG Grid, the Dutch e-Science Grid, which is financially supported by NWO.",

year = "2011",

month = jul,

doi = "10.1093/bioinformatics/btr316",

language = "English",

volume = "27",

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AU - Dutilh, Bas E.

AU - Jurgelenaite, Rasa

AU - Szklarczyk, Radek

AU - van Hijum, Sacha A.F.T.

AU - Harhangi, Harry R.

AU - Schmid, Markus

AU - de Wild, Bart

AU - Françoijs, Kees Jan

AU - Stunnenberg, Hendrik G.

AU - Strous, Marc

AU - Jetten, Mike S.M.

AU - Op den Camp, Huub J.M.

AU - Huynen, Martijn A.

N1 - Funding Information: Funding: B.E.D. was supported by the Netherlands Organisation for Scientific Research (NWO) Horizon grant (050-71-058) and by NWO Veni grant (016.111.075). R.J. was supported through the Virgo consortium (BSIK 03012), an Innovative Cluster approved by the Netherlands Genomics Initiative. R.S. was supported by NWO Horizon grant (050-71-053). M.Sc. was supported by the Darwin Center for Biogeosciences (project 142.16.1091). M.St. was supported by European Research Council starting grant MASEM (242635). This work is part of the programme of BiG Grid, the Dutch e-Science Grid, which is financially supported by NWO.

PY - 2011/7

Y1 - 2011/7

N2 - 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.

AB - 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.

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FACIL: Fast and accurate genetic code inference and logo

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