EuMicroSat db : A database for microsatellites in the sequenced genomes of eukaryotes.(Database)

Authors: Veenu Aishwarya [1]; Atul Grover [1,2]; Prakash C Sharma (corresponding author) [1]

Background

Microsatellites, also called as simple sequence repeats (SSRs) or simple tandem repeats (STRs) are ubiquitous component of eukaryotic genomes. A microsatellite consists of a specific sequence of DNA which contains 1-6 bp long (mono- to hexa- nucleotide) tandem repeats viz. (A)

16 , (GA)20 , (GATA)30 . Over the years, molecular biologists have increasingly exploited these sequences for diverse applications.

With the whole genome sequencing initiatives of various eukaryotic organisms, large amount of genomic sequence data has accumulated over the last few years. These sequence resources available in the public domain have also served as an attractive source of

in silico mining of microsatellite sequences [1, 2, 3, 4, 5]. In silico mining of these sequences offers advantage in terms of time, labour and cost over conventional isolation from genomic libraries. Similarly, ESTs have also been screened for the presence of microsatellites [6, 7, 8]. However, finding potentially useful microsatellites occupying specific genomic regions still remains a challenge for the molecular biologists. Availability of this information can facilitate molecular mapping of desired traits and preparation of linkage maps saturated with evenly distributed SSR markers.

Popularity of

in silico mining methods has led to the construction of various microsatellite databases in recent years, each with a different emphasis. For instance, MICdb [9] provides information on microsatellites spanning coding and non-coding regions, their frequency, size and repeat sequence. A recent version of this database covers 19 archeal, 155 eubacterial and 287 viral genomes. SilkSatDb [10] incorporates microsatellites extracted from the available ESTs and genomic sequences of the silkmoth (Bombyx mori ). This database also stores data on polymorphism status of different microsatellite loci. Similarly, mouse genomic microsatellites are collected in the Mouse Microsatellite Database of Japan (MMDBJ) [11]. CMD (Cotton Microsatellite Database) is a web-based relational database providing centralized access to publicly available cotton microsatellites. The database also provides a useful resource for mapping and related data pertaining to major cotton microsatellite projects [12]. Satellog [13] database catalogues triplet repeats associated with human disorders. Similarly Microsat2006 [14] database catalogues human microsatellite repeats. Taiwanese Polymorphic Microsatellite Database (TPMD) provides data on microsatellite mapping in the Taiwanese populations [15]. Molecular Mycology Research Laboratory, Westmead, Australia has created an SSR database [16] that …