Methods of Identification of Pseudogenes Based on Functionality: Hybridization of 18S rRNA and mRNA During Translation
Protein-coding sequences are characterized by a period-3 free energy signal that arises from the interaction between the 3′-terminal nucleotides of the 18S rRNA and the mRNA. Such a signal is not present in noncoding sequences such as introns and intergenic regions and can be used for pseudogene identification.
Key wordsHybridization of 18S rRNA and mRNA Secondary structure Free energy Cumulative sinusoidal wave Period-3 signal Amplitude Phase Pseudogene prediction
- 1.Xing C, Bitzer D, Alexander W, Stomp A-M, Vouk M (2006) Free energy analysis on the coding region of the individual gene of Saccharomyces cerevisiae. In: 28th annual international conference of the IEEE engineering in medicine and biology society, New York, NY, U S A, 30 Aug–3 Sept 2006, p –4228Google Scholar
- 2.Xing C, Mishra M, Vu SK, Alexander W, Bitzer D, Vouk M (2004) Free energy based analysis of the coding region of Saccharomyces cerevisiae. NC symposium on biotechnology & bioinformatics, Research Triangle Park, NC, U S A, 12–15 Oct 2004, p –27Google Scholar
- 4.Xing C (2007) Analysis and identification of protein-coding sequences for yeast using signal processing approaches. North Carolina State University, Raleigh, NCGoogle Scholar
- 10.Jaeger J, Turner JD, Zuker M (1986) Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A 37:7706–7710Google Scholar
- 11.Dash D, Gopalakrishnan V (2001) Modeling DNA splice regions by learning bayesian networks. Technical report, Center for Biomedical Informatics, University of PittsburghGoogle Scholar