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

Veenu Aishwarya,Prakash C Sharma,Atul Grover

doi:10.1186/1471-2164-8-225

Veenu Aishwarya, Prakash C Sharma + Show 1 more

Open Access

https://doi.org/10.1186/1471-2164-8-225

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Abstract

BackgroundMicrosatellites 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) is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes.DescriptionA 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.ConclusionThe 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.

Highlights

Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology
A collection of whole genome eukaryotic microsatellite data at a single platform is still not available. Recognizing this gap, we have developed a comprehensive database for easy retrieval of information on microsatellites distributed in the sequenced eukaryotic genomes
EuMicroSatdb database can be searched using following need based input parameters: Repeat unit length: the basic unit that is tandemly repeated in the microsatellite ranging from mononucleotide to hexanucleotide; Repeat sequence: this parameter allows the user to search microsatellite for a specific base sequence, for example, AT, GCG, etc.; Repeat number: is used to search microsatellites on the basis of repeat number of the microsatellite e.g. (CCT)9 has a repeat number of 9, (AGAGG)10 has a repeat number of 10; Microsatellite length: searches microsatellites on the basis of their total length in base pairs e.g. (TTGCA)5 has a length of 25 bp; Position: defined locations on the chromosome in terms of base pairs can be specified; Microsatellite cluster: search can be performed to look for adjacent microsatellites

Summary

Conclusion

EuMicrosatdb has been developed for genome wide mining of microsatellite in 31 completely sequenced eukaryotic genomes considering the immense utility of these sequences for a variety of experiments. Various parameters have been carefully inducted to allow comprehensive search of simple and compound microsatellites and to identify microsatellite clusters across the genomes. EuMicroSatdb will provide a useful resource for mining microsatellites to be used in gene tagging, comparative genomics and genetic diversity based studies in different genomes. W Figeubrient4erface for searching compound microsatellite Web interface for searching compound microsatellite. Web interface showing (A) various input parameters used for searching compound microsatellite, and (B) output of the query. VA was mainly responsible for writing codes, designing the architecture of the database and execution of the study. AG participated in designing of the database and helped in the preparation of the manuscript.

Background

Utility and Discussion