Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs
2008
OAF: A Tool for Detecting Antizymes in mRNA
Sample size: 6639
publication
Evidence: moderate
Author Information
Author(s): Bekaert Michaël, Ivanov Ivaylo P, Atkins John F, Baranov Pavel V
Primary Institution: University College Dublin
Hypothesis
Can a computer tool accurately detect antizyme coding sequences in mRNAs with frameshifts?
Conclusion
OAF effectively identifies antizyme sequences in mRNA and EST data, facilitating genome annotation.
Supporting Evidence
- OAF detected 6639 antizyme sequences in ESTs, including 2067 unique sequences.
- The tool was tested on 20 completed eukaryotic genomes, successfully identifying 18 OAZ genes.
- OAF outputs sequence annotations in various formats including fasta and XML.
Takeaway
The OAF tool helps scientists find important proteins in genetic material quickly and easily.
Methodology
OAF uses profile hidden Markov models to identify antizyme coding sequences from a set of known sequences.
Limitations
The tool may not detect all antizyme sequences due to the complexity of ribosomal frameshifting.
Digital Object Identifier (DOI)
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