title: ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting.
abstract: Correct annotation of genes encoding release factors in bacterial genomes is often complicated by utilization of +1 programmed ribosomal frameshifting during synthesis of release factor 2, RF2. In the absence of robust computational approaches for predicting ribosomal frameshifting, the success of proper annotation depends on annotators' familiarity with this phenomenon. Here we describe a novel computer tool that allows automatic discrimination of genes encoding class-I bacterial release factors, RF1, RF2 and RFH. Most usefully, this program identifies and automatically annotates +1 frameshifting in RF2 encoding genes. Comparison of ARFA performance with existing annotations of bacterial genomes revealed that only 20% of RF2 genes utilizing ribosomal frameshifting during their expression are annotated correctly.
  
  
  BACKGROUND
  The PHP based web interface of ARFA and the source code are located at http://recode.genetics.utah.edu/arfa
authors.affiliation: Biosciences Institute, University College Cork, Cork, Ireland.
authors.forename: Michaël
authors.initials: M
authors.lastname: Bekaert
authors.forename: John F
authors.initials: JF
authors.lastname: Atkins
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D004282:Documentation / Q000379:methods; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D018965:Frameshifting, Ribosomal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods; D008969:Molecular Sequence Data; D010454:Peptide Termination Factors / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D010454:Peptide Termination Factors; C041460:peptide chain termination release factor 2; C489006:prfB protein, E coli