title: FACIL: Fast and Accurate Genetic Code Inference and Logo.
abstract: BACKGROUND
  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.
  
  
  METHODS
  FACIL is available as a web-based service at http://www.cmbi.ru.nl/FACIL/ and as a stand-alone program.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, Germany. dutilh@cmbi.ru.nl
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.forename: Rasa
authors.initials: R
authors.lastname: Jurgelenaite
authors.forename: Radek
authors.initials: R
authors.lastname: Szklarczyk
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
authors.forename: Harry R
authors.initials: HR
authors.lastname: Harhangi
authors.forename: Markus
authors.initials: M
authors.lastname: Schmid
authors.forename: Bart
authors.initials: B
authors.lastname: de Wild
authors.forename: Kees-Jan
authors.initials: KJ
authors.lastname: Françoijs
authors.forename: Hendrik G
authors.initials: HG
authors.lastname: Stunnenberg
authors.forename: Marc
authors.initials: M
authors.lastname: Strous
authors.forename: Mike S M
authors.initials: MS
authors.lastname: Jetten
authors.forename: Huub J M
authors.initials: HJ
authors.lastname: Op den Camp
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Huynen
mesh_terms: D001483:Base Sequence / Q000235:genetics; D004247:DNA / Q000235:genetics; D030561:Databases, Nucleic Acid; D056908:Foraminifera / Q000235:genetics; D005815:Genetic Code; D020407:Internet; D008928:Mitochondria / Q000235:genetics; D011506:Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000295:instrumentation*; D012984:Software
chemical_list: D011506:Proteins; D004247:DNA