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UgMicroSatdb: database for mining microsatellites from unigenes.

Veenu Aishwarya1, P C Sharma

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

Nucleic Acids Research
|October 20, 2007
PubMed
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We developed UgMicroSatdb, a database of microsatellites in unigene sequences from 80 genomes. This tool aids research in gene regulation and genome evolution by enabling detailed microsatellite searches and primer design.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Microsatellites, or simple sequence repeats (SSRs)/short tandem repeats (STRs), are vital molecular markers.
  • Their significance in gene regulation and genome evolution is increasingly recognized.

Purpose of the Study:

  • To develop UgMicroSatdb, a comprehensive web-based database for microsatellites in unigene sequences.
  • To facilitate microsatellite analysis across 80 diverse genomes.

Main Methods:

  • Developed a relational database (UgMicroSatdb) integrating microsatellite data from 80 genomes.
  • Implemented versatile search functionalities based on microsatellite type, repeat characteristics, and sequence identifiers (EST, cDNA, CDS, Gene Index, GenBank, UniGene IDs).
  • Included features for analyzing trinucleotide repeats encoding amino acids and providing UniGene sequences for primer design.

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Main Results:

  • UgMicroSatdb provides a searchable repository of microsatellites across 80 genomes.
  • The database supports detailed queries by microsatellite type, length, repeat number, and sequence class.
  • Enables retrieval of codon repeats based on amino acid properties and facilitates PCR primer design.

Conclusions:

  • UgMicroSatdb serves as a valuable resource for microsatellite research.
  • The database enhances studies on gene regulation, genome evolution, and molecular marker applications.
  • Facilitates efficient primer design for microsatellite amplification and analysis.