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

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

Sub Bioinformatics

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

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.

Original language	English
Pages (from-to)	1929-1933
Number of pages	5
Journal	Bioinformatics
Volume	27
Issue number	14
Publication status	Published - 2011

Keywords

DNA
protein
article
computer program
DNA sequence
foraminifer
genetic code
genetics
devices
Internet
mitochondrion
nucleic acid database
nucleotide sequence

Cite this

@article{27370accb8fd4038831e95546ebd8f95,

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

keywords = "DNA, protein, article, computer program, DNA sequence, foraminifer, genetic code, genetics, devices, Internet, mitochondrion, nucleic acid database, nucleotide sequence",

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 Kees-Jan Fran{\c c}oijs and Stunnenberg, \{Hendrik G\} and Marc Strous and Jetten, \{Mike S M\} and \{Op den Camp\}, \{Huub J M\} and Huynen, \{Martijn A\}",

year = "2011",

language = "English",

volume = "27",

pages = "1929--1933",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "14",

}

TY - JOUR

T1 - FACIL: Fast and Accurate Genetic Code Inference and Logo.

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

PY - 2011

Y1 - 2011

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

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

KW - DNA

KW - protein

KW - article

KW - computer program

KW - DNA sequence

KW - foraminifer

KW - genetic code

KW - genetics

KW - devices

KW - Internet

KW - mitochondrion

KW - nucleic acid database

KW - nucleotide sequence

M3 - Article

C2 - 21653513

SN - 1367-4803

VL - 27

SP - 1929

EP - 1933

JO - Bioinformatics

JF - Bioinformatics

IS - 14

ER -

FACIL: Fast and Accurate Genetic Code Inference and Logo.

Abstract

Keywords

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