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Open Access Highly Accessed Database

EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

Veenu Aishwarya1, Atul Grover12 and Prakash C Sharma1*

Author Affiliations

1 University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi 110 006, India

2 Shri Radha Kissen Kanoria Center for Advanced Studies in Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali 304 022 (Raj.) India

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BMC Genomics 2007, 8:225  doi:10.1186/1471-2164-8-225

Published: 10 July 2007

Abstract

Background

Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSatdb (Eukaryotic MicroSatellite database) http://ipu.ac.in/usbt/EuMicroSatdb.htm webcite is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes.

Description

A user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP). The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided.

Conclusion

The database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.