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Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs

BMC Bioinformatics
Springer (Biomed Central Ltd.)
Publication Date
DOI: 10.1186/1471-2105-9-178
  • Software
  • Biology
  • Chemistry
  • Computer Science
  • Medicine

Abstract ral ss BioMed CentBMC Bioinformatics Open AcceSoftware Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs Michaël Bekaert1, Ivaylo P Ivanov2, John F Atkins2,3 and Pavel V Baranov*4 Address: 1School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland, 2Bioscience Institute, University College Cork, Cork, Ireland, 3Human Genetics Department, University of Utah, Salt Lake City, Utah, USA and 4Biochemistry Department, University College Cork, Cork, Ireland Email: Michaël Bekaert - [email protected]; Ivaylo P Ivanov - [email protected]; John F Atkins - [email protected]; Pavel V Baranov* - [email protected] * Corresponding author Abstract Background: Ornithine decarboxylase antizymes are proteins which negatively regulate cellular polyamine levels via their affects on polyamine synthesis and cellular uptake. In virtually all organisms from yeast to mammals, antizymes are encoded by two partially overlapping open reading frames (ORFs). A +1 frameshift between frames is required for the synthesis of antizyme. Ribosomes change translation phase at the end of the first ORF in response to stimulatory signals embedded in mRNA. Since standard sequence analysis pipelines are currently unable to recognise sites of programmed ribosomal frameshifting, proper detection of full length antizyme coding sequences (CDS) requires conscientious manual evaluation by a human expert. The rapid growth of sequence information demands less laborious and more cost efficient solutions for this problem. This manuscript describes a rapid and accurate computer tool for antizyme CDS detection that requires minimal human involvement. Results: We have developed a computer tool, OAF (ODC antizyme finder) for identifying antizyme encoding sequences in spliced or intronless nucleic acid sequenes. OAF utilizes a combination of profile hidden Markov models (HMM) built separately

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