Introduction

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

Publications

  1. FACIL: Fast and Accurate Genetic Code Inference and Logo.
    Cite this
    Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA, 2011-07-01 - Bioinformatics (Oxford, England)

Credits

  1. Bas E Dutilh
    Developer

    Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences

  2. Rasa Jurgelenaite
    Developer

  3. Radek Szklarczyk
    Developer

  4. Sacha A F T van Hijum
    Developer

  5. Harry R Harhangi
    Developer

  6. Markus Schmid
    Developer

  7. Bart de Wild
    Developer

  8. Kees-Jan Françoijs
    Developer

  9. Hendrik G Stunnenberg
    Developer

  10. Marc Strous
    Developer

  11. Mike S M Jetten
    Developer

  12. Huub J M Op den Camp
    Developer

  13. Martijn A Huynen
    Investigator

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Summary
AccessionBT000669
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByMartijn A Huynen