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EuMicroSatdb: a database for microsatellites in the sequenced genomes of eukaryotes
Veenu Aishwarya1, Atul Grover, Prakash C Sharma
1University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi, India. veenu_aishwarya@yahoo.com <veenu_aishwarya@yahoo.com>
BMC Genomics
|July 12, 2007
Summary
EuMicroSatdb is a new eukaryotic microsatellite database providing efficient positional mining of microsatellites. This resource aids researchers in genome characterization, mapping, and understanding microsatellite dynamics.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Microsatellites are valuable molecular markers for genome characterization, mapping, phylogeny, and evolutionary biology.
- Existing microsatellite databases offer limited utility due to content and information output constraints.
- EuMicroSatdb (Eukaryotic MicroSatellite database) is a web-based relational database for efficient microsatellite mining from eukaryotic genomes.
Purpose of the Study:
- To develop a user-friendly web-based database for retrieving microsatellite information.
- To facilitate positional mining of microsatellites from sequenced eukaryotic genomes.
- To provide comprehensive data for various research applications.
Main Methods:
- Developed a user-friendly web interface using Active Server Pages (ASP).
- Utilized Perl-based scripts and C++ for backend database operations.
- Implemented retrieval based on microsatellite type, repeat unit length, repeat number, length, and chromosomal location.
Main Results:
- EuMicroSatdb enables systematic retrieval of comprehensive microsatellite information.
- The database includes data on simple and compound microsatellites, clusters, and locus coordinates for 31 eukaryotic genomes.
- Provides 200 bp flanking sequences for primer design for PCR amplification.
Conclusions:
- The database facilitates easy and systematic retrieval of microsatellite data.
- EuMicroSatdb supports research in gene tagging, genome mapping, population genetics, and germplasm characterization.
- Enhances understanding of microsatellite dynamics in eukaryotic genomes.
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