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Related Experiment Video

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A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

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Published on: November 3, 2011

Predicting polymorphic EST-SSRs in silico.

Chris Duran1, Richa Singhania, Harsh Raman

  • 1Melbourne eResearch Group, University of Melbourne, Parkville, Vic, 3010, Australia.

Molecular Ecology Resources
|February 13, 2013
PubMed
Summary
This summary is machine-generated.

Researchers identified 597 potential Simple Sequence Repeat (SSR) markers from barley gene sequences. These markers are valuable for genetic analysis and can be used across different species.

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Area of Science:

  • Genetics
  • Bioinformatics

Background:

  • Large-scale gene sequence data is publicly available, offering opportunities for genetic marker discovery.
  • Simple Sequence Repeats (SSRs) are valuable genetic markers due to their low cost, ease of production, and potential association with annotated genes.

Purpose of the Study:

  • To characterize barley expressed sequence tag SSRs (EST-SSRs).
  • To identify polymorphic SSRs from expressed sequence tag data for genetic analysis.

Main Methods:

  • Polymorphic SSRs were identified by analyzing varying motif lengths in aligned sequence reads.
  • Confidence in polymorphisms was assessed using redundancy and co-segregation measures.
  • Primers were designed for identified SSRs and validated for polymorphism and cross-species transferability.

Main Results:

  • 597 candidate polymorphic SSRs were discovered from 452,642 consensus expressed sequences.
  • Ten primer pairs showed polymorphism in barley and cross-species transferability.
  • Analysis included SSR motif, length, position, and annotation.

Conclusions:

  • The study successfully identified and validated a significant number of polymorphic EST-SSRs in barley.
  • These markers are suitable for genetic analysis and demonstrate potential for cross-species applications.