MSDB: a user-friendly program for reporting distribution and building databases of microsatellites from genome sequences.

Microsatellite Search and Building Database (MSDB) is a new Perl program providing a user-friendly interface for identification and building databases of microsatellites from complete genome sequences. The general aims of MSDB are to use the database to store the information of microsatellites and to facilitate the management, classification, and statistics of microsatellites. A user-friendly interface facilitates the treatment of large datasets. The program is powerful in finding various types of pure, compound, and complex microsatellites from sequences as well as generating a detailed statistical report in worksheet format. MSDB also contains other two subprograms: SWR, which is used to export microsatellites from the database to meet user's requirements, and SWP, which is used to automatically invoke R to draw a sliding window plot for displaying the distribution of density or frequency of identified microsatellites. MSDB is freely available under the GNU General Public license for Windows and Linux from the following website: http://msdb.biosv.com/.

[1]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[2]  Zhihe Zhang,et al.  Development of new tetranucleotide microsatellite loci and assessment of genetic variation of giant panda in two largest giant panda captive breeding populations , 2010 .

[3]  G. Chambers,et al.  Microsatellites: consensus and controversy. , 2000, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[4]  Yidong Chen,et al.  GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus , 2008, Bioinform..

[5]  W R Pearson,et al.  Using the FASTA program to search protein and DNA sequence databases. , 1994, Methods in molecular biology.

[6]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[7]  E. Danchin,et al.  Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita , 2010, BMC Genomics.

[8]  Jifeng Tang,et al.  Analysis of microsatellites in major crops assessed by computational and experimental approaches , 2003, Molecular Breeding.

[9]  R. Varshney,et al.  Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) , 2003, Theoretical and Applied Genetics.

[10]  L. Zane,et al.  Strategies for microsatellite isolation: a review , 2002, Molecular ecology.

[11]  Gregory Kucherov,et al.  mreps: efficient and flexible detection of tandem repeats in DNA , 2003, Nucleic Acids Res..

[12]  Guang R. Gao,et al.  TROLL-Tandem Repeat Occurrence Locator , 2002, Bioinform..

[13]  L. Lipovich,et al.  Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. , 2001, Genome research.

[14]  Emese Meglécz,et al.  QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects , 2010, Bioinform..

[15]  Hampapathalu A. Nagarajaram,et al.  Genome analysis IMEx : Imperfect Microsatellite Extractor , 2007 .

[16]  Robert Kofler,et al.  SciRoKo: a new tool for whole genome microsatellite search and investigation , 2007, Bioinform..

[17]  B. Faircloth,et al.  msatcommander: detection of microsatellite repeat arrays and automated, locus‐specific primer design , 2008, Molecular ecology resources.

[18]  H. Ellegren.  Microsatellites: simple sequences with complex evolution , 2004, Nature Reviews Genetics.

[19]  L. Bachmann,et al.  Allelic variation, fragment length analyses and population genetic models: a case study on Drosophila microsatellites* , 2004 .