Review
doi: 10.1089/cmb.2005.12.928.
Finding approximate tandem repeats in genomic sequences
Affiliations
- PMID: 16201913
- DOI: 10.1089/cmb.2005.12.928
Item in Clipboard
Review
Finding approximate tandem repeats in genomic sequences
J Comput Biol.
2005 Sep.
Abstract
An efficient algorithm is presented for detecting approximate tandem repeats in genomic sequences. The algorithm is based on a flexible statistical model which allows a wide range of definitions of approximate tandem repeats. The ideas and methods underlying the algorithm are described and its effectiveness on genomic data is demonstrated.
Similar articles
-
A novel approach to the detection of genomic approximate tandem repeats in the Levenshtein metric.J Comput Biol. 2007 Sep;14(7):873-91. doi: 10.1089/cmb.2007.0018. J Comput Biol. 2007. PMID: 17803368
-
Spectral-Statistical Approach for Revealing Latent Regular Structures in DNA Sequence.Methods Mol Biol. 2016;1415:315-40. doi: 10.1007/978-1-4939-3572-7_16. Methods Mol Biol. 2016. PMID: 27115640
-
Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences.Math Biosci. 2008 Jan;211(1):186-204. doi: 10.1016/j.mbs.2007.10.008. Epub 2007 Nov 5. Math Biosci. 2008. PMID: 18062999
-
Key-string algorithm--novel approach to computational analysis of repetitive sequences in human centromeric DNA.Croat Med J. 2003 Aug;44(4):386-406. Croat Med J. 2003. PMID: 12950141 Review.
-
Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences.Mol Biosyst. 2015 Oct;11(10):2620-34. doi: 10.1039/c5mb00155b. Mol Biosyst. 2015. PMID: 26099739 Review.
Cited by
-
Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel). 2024 Sep 19;13(18):2619. doi: 10.3390/plants13182619. Plants (Basel). 2024. PMID: 39339594 Free PMC article. Review.
-
Significant deviations in the configurations of homologous tandem repeats in prokaryotic genomes.Genomics Proteomics Bioinformatics. 2009 Dec;7(4):163-74. doi: 10.1016/S1672-0229(08)60046-7. Genomics Proteomics Bioinformatics. 2009. PMID: 20172489 Free PMC article.
-
VNTRDB: a bacterial variable number tandem repeat locus database.Nucleic Acids Res. 2007 Jan;35(Database issue):D416-21. doi: 10.1093/nar/gkl872. Epub 2006 Dec 14. Nucleic Acids Res. 2007. PMID: 17175529 Free PMC article.
-
Dot2dot: accurate whole-genome tandem repeats discovery.Bioinformatics. 2019 Mar 15;35(6):914-922. doi: 10.1093/bioinformatics/bty747. Bioinformatics. 2019. PMID: 30165507 Free PMC article.
-
Advances in the discovery and analyses of human tandem repeats.Emerg Top Life Sci. 2023 Dec 14;7(3):361-381. doi: 10.1042/ETLS20230074. Emerg Top Life Sci. 2023. PMID: 37905568 Free PMC article. Review.
Publication types
MeSH terms
LinkOut - more resources
Full Text Sources
