Searching microsatellites in DNA sequences: Approaches used and tools developed

被引：22

作者：

Grover A. ^{[1
,2
]}

Aishwarya V. ^{[1
,3
]}

Sharma P.C. ^{[1
]}

机构：

[1] University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi 110075

[2] Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio Energy Research, Haldwani 263139, Goraparao

[3] Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA

来源：

Physiology and Molecular Biology of Plants | 2012年 / 18卷 / 1期

关键词：

Deterministic approaches; Microsatellites; Mining tools; Stochastic models;

D O I：

10.1007/s12298-011-0098-y

中图分类号：

学科分类号：

摘要：

Microsatellite instability associated genomic activities and evolutionary changes have led to a renewed focus on microsatellite research. In last decade, a number of microsatellite mining tools have been introduced based on different computational approaches. The choice is generally made between slow but exhaustive dynamic programming based approaches, or fast and incomplete heuristic methods. Tools based on stochastic approaches are more popular due to their simplicity and added ornamental features. We have performed a comparative evaluation of the relative efficiency of some microsatellite search tools with their default settings. The graphical user interface, the statistical analysis of the output and ability to mine imperfect repeats are the most important criteria in selecting a tool for a particular investigation. However, none of the available tools alone provides complete and accurate information about microsatellites, and a lot depends on the discretion of the user. © 2011 Prof. H.S. Srivastava Foundation for Science and Society.

引用

页码：11 / 19

页数：8

共 70 条

[1]

Agarwal M., Shrivastava N., Padh H., Advances in molecular marker techniques and their applications in plant sciences, Plant Cell Rep, 27, pp. 617-631, (2008)

[2]

Bagshaw A.T.M., Pitt J.P.W., Gemmell N.J., Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots, BMC Genomics, 7, (2006)

[3]

Bagshaw A.T.M., Pitt J.P.W., Gemmell N.J., High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots, BMC Genomics, 9, (2008)

[4]

Bai X., Zhang W., Ornates L., Jun T., Mittapalli O., Mian M.A.R., Michael A.P., Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines, PLoS One, 5, (2010)

[5]

Benson G., Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Res, 27, pp. 573-580, (1999)

[6]

Benson G., Tandem cyclic alignment, Discret Appl Math, 146, pp. 124-133, (2005)

[7]

Benson G., Waterman M.S., A method for fast database search for all k-nucleotide repeats, Nucleic Acids Res, 22, pp. 4828-4836, (1994)

[8]

Bilgen M., Karaca M., Onus A.N., Ince A.G., A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences, Bioinformatics, 20, pp. 3379-3386, (2004)

[9]

Bizzaro J.W., Marx K.A., Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA, BMC Bioinforma, 4, (2003)

[10]

Boeva V., Regnier M., Papatsenko D., Makeev V., Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression, Bioinformatics, 22, pp. 676-684, (2006)

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