Release Factor Annotation

In majority of bacteria, release factor 2 is synthesized via +1 programmed ribosomal frameshifting. This complicates proper annotation of corresponding genes in bacterial genomes. Further hurdle is the existence of a conserved gene (known as prfH or RFH) in a small proportion of bacteria which is a homolog of standard factors RF1 and RF2. Frequently this gene is missannotated as an additional RF2. To overcome these problems in annotation of release factors we developed ARFA.

Automated Release Factor Annotation

Automated Release Factor Annotation (ARFA) is a software tool for identification of genes encoding class I bacterial release factors. As input, it takes nucleotide sequences in fasta format or Genbank accession numbers. If ARFA identifies a gene encoding release factor, it generates its annotation in genbank or XML formats. A unique feature of ARFA is its ability to predict programmed ribosomal frameshifting that takes place during expression of genes encoding bacterial release factor 2.

You could use ARFA via the web interface. It is also possible to download and install it locally. You will need Bioperl, Fasta and HMMER.

Citation and Commercial Use

If you use ARFA for your research, please cite the following paper: Bekaert M, Atkins JF & Baranov PV (2006) ARFA: A program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting. Bioinformatics, published on-line ahead of print (abstract, PDF).

If you plan to use ARFA for commercial purposes, please, contact the authors to arrange a proper permission.

xhtml - css