Localizing triplet periodicity in DNA and cDNA sequences

Wang, L., Stein, L. D. (2010) Localizing triplet periodicity in DNA and cDNA sequences. BMC Bioinformatics, 11. p. 550. ISSN 1471-2105 (Electronic) 1471-2105 (Linking)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21059240 http:/...
DOI: 10.1186/1471-2105-11-550

Abstract

BACKGROUND: The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is divided into small segments and a Fourier Transform is applied on each segment, a strong peak at frequency 1/3 is typically observed in the Fourier spectrum of coding segments, but not in non-coding regions. This property has been used in identifying the locations of protein-coding genes in unannotated sequence. The method is fast and requires no training. However, the need to compute the Fourier Transform across a segment (window) of arbitrary size affects the accuracy with which one can localize TP boundaries. Here, we report a technique that provides higher-resolution identification of these boundaries, and use the technique to explore the biological correlates of TP regions in the genome of the model organism C. elegans. RESULTS: Using both simulated TP signals and the real C. elegans sequence F56F11 as an example, we demonstrate that, (1) Modified Wavelet Transform (MWT) can better define the boundary of TP region than the conventional Short Time Fourier Transform (STFT); (2) The scale parameter (a) of MWT determines the precision of TP boundary localization: bigger values of a give sharper TP boundaries but result in a lower signal to noise ratio; (3) RNA splicing sites have weaker TP signals than coding region; (4) TP signals in coding region can be destroyed or recovered by frame-shift mutations; (5) 6 bp periodicities in introns and intergenic region can generate false positive signals and it can be removed with 6 bp MWT. CONCLUSIONS: MWT can provide more precise TP boundaries than STFT and the boundaries can be further refined by bigger scale MWT. Subtraction of 6 bp periodicity signals reduces the number of false positives. Experimentally-introduced frame-shift mutations help recover TP signal that have been lost by possible ancient frame-shifts. More importantly, TP signal has the potential to be used to detect the splice junctions in fully spliced mRNA sequence.

Item Type: Paper
Uncontrolled Keywords: Animals Base Sequence Caenorhabditis elegans/genetics DNA/ chemistry DNA, Complementary/ chemistry Fourier Analysis Introns RNA Splicing Sequence Analysis, DNA/ methods
Subjects: bioinformatics > genomics and proteomics > alignment > sequence alignment
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date Deposited: 20 Oct 2011 13:55
Last Modified: 29 Nov 2011 20:03
PMCID: PMC:2992068
URI: http://repository.cshl.edu/id/eprint/15580

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