Peer-Reviewed Journal Details
Mandatory Fields
Bekaert M, Atkins JF, Baranov PV;
2006
October
Bioinformatics (Oxford, England)
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting.
Validated
Optional Fields
22
20
2463
2465
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. AVAILABILITY: The PHP based web interface of ARFA and the source code are located at http://recode.genetics.utah.edu/arfa
10.1093/bioinformatics/btl430
Grant Details