In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes

被引：19

作者：

Alam, Chaudhary Mashhood ^{[1
]}

Singh, Avadhesh Kumar ^{[2
]}

Sharfuddin, Choudhary ^{[1
]}

Ali, Safdar ^{[2
]}

机构：

[1] Univ Patna, Dept Bot, Patna 800005, Bihar, India

[2] Univ Delhi, SRCASW, Dept Biomed Sci, New Delhi 110096, India

来源：

GENE | 2013年 / 530卷 / 02期

关键词：

Tobamovirus; Simple sequence repeats; IMEx; dMAX; Correlation studies; SIMPLE SEQUENCE REPEATS; TANDEM REPEATS; MUTATIONS; EXPANSION; POLYMORPHISM; GENES; DNA;

D O I：

10.1016/j.gene.2013.08.046

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

An in-silico analysis of simple sequence repeats (SSRs) in 30 species of tobamoviruses was done. SSRs (mono to hexa) were present with variant frequency across species. Compound microsatellites, primarily of variant motifs accounted for up to 11.43% of the SSRs. Motif duplications were observed for A, T, AT, and ACA repeats. (AG)-(TC) was the most prevalent SSR-couple. SSRs were differentially localized in the coding region with similar to 54% on the 128 kDa protein while 20.37% was exclusive to 186 kDa protein. Characterization of such variations is important for elucidating the origin, sequence variations, and structure of these widely used, but incompletely understood sequences. (c) 2013 Elsevier B.V. All rights reserved.

引用

页码：193 / 200

页数：8

共 48 条

[1] Occurrence and analysis of imperfect microsatellites in diverse potyvirus genomes [J].

Alam, Ch. Mashhood ;

George, B. ;

Sharfuddin, Ch. ;

Jain, S. K. ;

Chakraborty, S. .

GENE, 2013, 521 (02) :238-244

[2]

Archak S, NUCL ACIDS RES, V35, pD36

[3] Tandem repeats in protein coding regions of primate genes [J].

Borstnik, B ;

Pumpernik, D .

GENOME RESEARCH, 2002, 12 (06) :909-915

[4] Compound microsatellite repeats:: Practical and theoretical features [J].

Bull, LN ;

Pabón-Peña, CR ;

Freimer, NB .

GENOME RESEARCH, 1999, 9 (09) :830-838

[5] Microsatellites: consensus and controversy [J].

Chambers, GK ;

MacAvoy, ES .

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY, 2000, 126 (04) :455-476

[6] Differential distribution of compound microsatellites in various Human Immunodeficiency Virus Type 1 complete genomes [J].

Chen, Ming ;

Tan, Zhongyang ;

Zeng, Guangming ;

Zeng, Zhuotong .

INFECTION GENETICS AND EVOLUTION, 2012, 12 (07) :1452-1457

[7] Compound microsatellites in complete Escherichia coli genomes [J].

Chen, Ming ;

Zeng, Guangming ;

Tan, Zhongyang ;

Jiang, Min ;

Zhang, Jiachao ;

Zhang, Chang ;

Lu, Lunhui ;

Lin, Yuzhen ;

Peng, Jun .

FEBS LETTERS, 2011, 585 (07) :1072-1076

[8] Similar distribution of simple sequence repeats in diverse completed Human Immunodeficiency Virus Type 1 genomes [J].

Chen, Ming ;

Tan, Zhongyang ;

Jiang, Jianhui ;

Li, Mingfu ;

Chen, Hongjun ;

Shen, Guoli ;

Yu, Ruqin .

FEBS LETTERS, 2009, 583 (17) :2959-2963

[9] Characterization of mononucleotide repeats in sequenced prokaryotic genomes [J].

Coenye, Tom ;

Vandamme, Peter .

DNA RESEARCH, 2005, 12 (04) :221-233

[10] Utilization of Microsatellite Polymorphism for Differentiating Herpes Simplex Virus Type 1 Strains [J].

Deback, C. ;

Boutolleau, D. ;

Depienne, C. ;

Luyt, C. E. ;

Bonnafous, P. ;

Gautheret-Dejean, A. ;

Garrigue, I. ;

Agut, H. .

JOURNAL OF CLINICAL MICROBIOLOGY, 2009, 47 (03) :533-540

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