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ESAP plus: a web-based server for EST-SSR marker development.

Piyarat Ponyared1, Jiradej Ponsawat2, Sissades Tongsima3

  • 1Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.

BMC Genomics
|February 4, 2017
PubMed
Summary

Researchers can now easily develop SSR markers from large Expressed Sequence Tag (EST) collections using ESAP Plus, a user-friendly web-based bioinformatics pipeline. This tool simplifies the identification of valuable molecular markers for plant genetic studies.

Keywords:
BioinformaticsEST-SSR development pipelineExpressed sequence tags (ESTs)Simple sequence repeats (SSRs)

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Area of Science:

  • Bioinformatics
  • Plant Genetics
  • Molecular Biology

Background:

  • Simple sequence repeats (SSRs) are crucial molecular markers in plant genetics due to their high variability.
  • Developing SSR markers from Expressed Sequence Tags (ESTs) is essential for plants lacking sequenced genomes.
  • Identifying SSRs from large EST datasets requires sophisticated, user-friendly computational pipelines.

Purpose of the Study:

  • To develop a web-based bioinformatics pipeline, ESAP Plus, for efficient EST-SSR marker development.
  • To provide researchers with an accessible tool for analyzing large EST collections.
  • To streamline the process of designing high-quality EST-SSR primers.

Main Methods:

  • ESAP Plus integrates bioinformatic scripts and standard software for EST pre-processing, clustering, SSR mining, and primer design.
  • The pipeline utilizes a web interface built with PHP, HTML, CSS, and Java scripts for user interaction.
  • Data is stored in a MySQL database, with email notifications and web-based download options for results.

Main Results:

  • ESAP Plus successfully processed public sugarcane ESTs, demonstrating its automated pipeline execution.
  • The tool offers adjustable filtering options and parameters for customized EST-SSR analysis.
  • Users can upload raw EST data, visualize, and download SSR information through the web interface.

Conclusions:

  • ESAP Plus is a comprehensive and convenient web-based tool for developing EST-SSR markers.
  • The pipeline efficiently handles large EST datasets, offering adjustable options for marker identification.
  • ESAP Plus provides an accessible solution for researchers needing to develop SSR markers from EST collections.