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Nucleic Acids Research Advance Access originally published online on October 18, 2007
Nucleic Acids Research 2008 36(Database issue):D53-D56; doi:10.1093/nar/gkm811
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Nucleic Acids Research, 2008, Vol. 36, Database issue D53-D56
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

UgMicroSatdb: database for mining microsatellites from unigenes

Veenu Aishwarya and P. C. Sharma*

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

*To whom correspondence should be addressed. Tel: +91 11 23900220; Fax: +91 11 23865941; Email: deansbt{at}yahoo.co.in

Received August 14, 2007. Revised September 17, 2007. Accepted September 18, 2007.

Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web-based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type (simple perfect, compound perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite. UgMicroSatdb is available at http://ipu.ac.in/usbt/UgMicroSatdb.htm.


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