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Literature DB >> 16201913

Finding approximate tandem repeats in genomic sequences.

Ydo Wexler¹, Zohar Yakhini, Yechezkel Kashi, Dan Geiger.

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.

Mesh：

Year: 2005 PMID： 16201913 DOI： 10.1089/cmb.2005.12.928

Source DB: PubMed Journal: J Comput Biol ISSN： 1066-5277 Impact factor: 1.479

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Cited

22 in total

1. A new way to visualize DNA's base succession: the Caenorhabditis elegans chromosome landscapes.

Authors: Afef Elloumi Oueslati; Imen Messaoudi; Zied Lachiri; Noureddine Ellouze
Journal: Med Biol Eng Comput Date: 2015-05-24 Impact factor: 2.602

2. Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards.

Authors: Nathalie Feiner
Journal: Proc Biol Sci Date: 2016-10-12 Impact factor: 5.349

3. HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.

Authors: Alexander Churbanov; Rachael Ryan; Nabeeh Hasan; Donovan Bailey; Haofeng Chen; Brook Milligan; Peter Houde
Journal: Bioinformatics Date: 2012-09-06 Impact factor: 6.937

4. A method for discovering common patterns from two RNA secondary structures and its application to structural repeat detection.

Authors: Lei Hua; Jason T L Wang; Xiang Ji; Ankur Malhotra; Mugdha Khaladkar; Bruce A Shapiro; Kaizhong Zhang
Journal: J Bioinform Comput Biol Date: 2012-06-22 Impact factor: 1.122

Finding approximate tandem repeats in genomic sequences.

1. A new way to visualize DNA's base succession: the Caenorhabditis elegans chromosome landscapes.

2. Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards.

3. HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.

4. A method for discovering common patterns from two RNA secondary structures and its application to structural repeat detection.

5. TRStalker: an efficient heuristic for finding fuzzy tandem repeats.

6. Indication for Co-evolution of Lactobacillus johnsonii with its hosts.

7. A monte carlo method for assessing the quality of duplication-aware alignment algorithms.

8. NTRFinder: a software tool to find nested tandem repeats.

9. A lossy compression technique enabling duplication-aware sequence alignment.

10. Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases.