ArticleEURASIP journal on bioinformatics & systems biology2007
A novel signal processing measure to identify exact and inexact tandem repeat patterns in DNA sequences.
Article in EURASIP journal on bioinformatics & systems biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 51 citations in OpenAlex.
- High-fidelity, large-scale targeted profiling of microsatellites.Genome research · 2024Article
- Finding long tandem repeats in long noisy reads.Bioinformatics (Oxford, England) · 2021Article
- Periodic power spectrum with applications in detection of latent periodicities in DNA sequences.Journal of mathematical biology · 2016Article
- Improved algorithm for analysis of DNA sequences using multiresolution transformation.TheScientificWorldJournal · 2015Article
- Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm.Nucleic acids research · 2013Article
- Searching microsatellites in DNA sequences: approaches used and tools developed.Physiology and molecular biology of plants : an international journal of functional plant biology · 2012Article
- Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties.BMC genomics · 2011Article
- TRStalker: an efficient heuristic for finding fuzzy tandem repeats.Bioinformatics (Oxford, England) · 2010Article
- Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.BMC bioinformatics · 2008Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification and analysis of repetitive patterns are active areas of biological and computational research. Tandem repeats in telomeres play a role in cancer and hypervariable trinucleotide tandem repeats are linked to over a dozen major neurodegenerative genetic disorders. In this paper, we present an algorithm to identify the exact and inexact repeat patterns in DNA sequences based on orthogonal exactly periodic subspace decomposition technique. Using the new measure our algorithm resolves the problems like whether the repeat pattern is of period P or its multiple (i.e., 2P, 3P, etc.), and several other problems that were present in previous signal-processing-based algorithms. We present an efficient algorithm of O(NL(w) log L(w)), where N is the length of DNA sequence and L(w) is the window length, for identifying repeats. The algorithm operates in two stages. In the first stage, each nucleotide is analyzed separately for periodicity, and in the second stage, the periodic information of each nucleotide is combined together to identify the tandem repeats. Datasets having exact and inexact repeats were taken up for the experimental purpose. The experimental result shows the effectiveness of the approach.
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Registered trials
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