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BMC Genomics. 2007 Jul 10;8:225.

EuMicroSatdb: a database for microsatellites in the sequenced genomes of eukaryotes.

Author information

1
University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi, India. veenu_aishwarya@yahoo.com <veenu_aishwarya@yahoo.com>

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 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.

PMID:
17623061
PMCID:
PMC1933429
DOI:
10.1186/1471-2164-8-225
[Indexed for MEDLINE]
Free PMC Article

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