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The ITS2 Database
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MSDB: A Comprehensive Database of Simple Sequence Repeats.

Akshay Kumar Avvaru1, Saketh Saxena1, Divya Tej Sowpati1

  • 1CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India.

Genome Biology and Evolution
|September 1, 2017
PubMed
Summary
This summary is machine-generated.

Microsatellites, or Simple Sequence Repeats (SSRs), are vital genome markers with regulatory roles. The MSDB database offers an extensive resource for analyzing over 650 million SSRs across diverse species.

Keywords:
DjangoJavaScriptdatabasegenomicsmicrosatellitessimple sequence repeats

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs found in all genomes, particularly eukaryotes.
  • SSRs serve as valuable genome markers and possess regulatory functions, with length variations in coding regions linked to human disorders.

Purpose of the Study:

  • To introduce the Microsatellite Database (MSDB) as a comprehensive resource for SSR data.
  • To provide a platform for accessing and analyzing SSRs from a wide range of species.

Main Methods:

  • Compilation of over 650 million SSRs from 6,893 species (Bacteria, Archaea, Fungi, Plants, Animals).
  • Development of a user-friendly interface using the Django framework and MySQL.
  • Implementation of customizable tabular data exploration and interactive multi-species plotting.

Main Results:

  • MSDB is the most exhaustive resource available for SSR data analysis across multiple species.
  • The database enables users to explore, view, and compare SSR data efficiently.

Conclusions:

  • MSDB significantly advances the study of microsatellites by providing a centralized and accessible platform.
  • The database facilitates research into the functional and evolutionary roles of SSRs in diverse taxa.