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SAT, a flexible and optimized Web application for SSR marker development.

Alexis Dereeper1, Xavier Argout, Claire Billot

  • 1CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, Montpellier, France. Alexis.Dereeper@igs.cnrs-mrs.fr

BMC Bioinformatics
|December 1, 2007
PubMed
Summary
This summary is machine-generated.

Simple Sequence Repeat (SSR) marker development is streamlined by the SSR Analysis Tool (SAT). This web application automates tedious tasks, reducing errors and accelerating the design of optimal SSR genetic markers from sequence data.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Molecular Biology

Background:

  • Simple Sequence Repeats (SSRs), also known as microsatellites, are highly informative genetic markers.
  • Developing SSR markers typically involves creating enriched genomic DNA libraries, followed by sequencing.
  • Manual analysis of bulk sequence data for SSR marker design is labor-intensive and prone to errors.

Purpose of the Study:

  • To introduce the SSR Analysis Tool (SAT), a user-friendly web application.
  • To automate and simplify the process of SSR marker development from sequence data.
  • To reduce manual effort and minimize errors in SSR marker design.

Main Methods:

  • SAT integrates, analyzes, and displays sequence data from SSR-enriched libraries.
  • The tool performs automated base calling, quality evaluation, vector/adaptor trimming, and chimera detection.
  • SAT identifies SSR motifs, clusters sequences, assembles redundant data, and designs SSR primer pairs with virtual PCR for specificity checks.

Main Results:

  • SAT automates complex bioinformatics tasks, significantly reducing the time and effort required for SSR marker development.
  • The application offers flexibility, allowing users to select specific analysis steps or run the entire pipeline.
  • A database functionality enables storage, querying, and re-execution of analysis steps for efficient data management.

Conclusions:

  • The SAT web application provides an efficient and user-friendly solution for SSR marker development.
  • SAT is accessible online at http://sat.cirad.fr/sat, with a downloadable command-line version available.
  • Users can obtain login credentials by emailing tropgene@cirad.fr.