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Related Experiment Videos

A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences.

Mehmet Bilgen1, Mehmet Karaca, A Naci Onus

  • 1Faculty of Agriculture, Akdeniz University, 07059 Antalya, Turkey.

Bioinformatics (Oxford, England)
|July 17, 2004
PubMed
Summary

Tandem repeats (TRs) are short DNA sequences found in genomes. A new software, TRA 1.5, efficiently identifies these repeats in expressed sequence tags (ESTs), aiding gene mapping and association studies.

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology

Background:

  • Genomes contain short tandemly repeated DNA sequences (tandem repeats, TRs) in both coding and non-coding regions.
  • Identifying TRs is crucial for gene mapping, association studies, and understanding gene expression under various conditions.
  • Existing repeat finder programs have limitations in file compatibility and analysis options.

Purpose of the Study:

  • To introduce Tandem Repeats Analyzer 1.5 (TRA), a novel PC-based software for identifying TRs.
  • To analyze TRs in expressed sequence tags (ESTs) across different Arabidopsis species and conditions.
  • To evaluate the utility of TRA for discovering TRs in coding and non-coding regions of genes.

Main Methods:

  • Developed TRA 1.5 software for motif searches combined with keywords (organs, tissues, etc.) to find exact, inexact, and compound TRs.

Related Experiment Videos

  • TRA 1.5 accepts GenBank, FASTA, and EST sequence files, supporting multifile and multisequence analysis.
  • Utilized advanced user-defined parameters for simultaneous motif length searches and statistical output evaluation.

    • Main Results:

    • Applied TRA to 175,899 EST sequences from three Arabidopsis species (A.lyrata, A.thaliana, A.halleri).
    • Determined EST-SSR/EST ratios: 43.1% in A.lyrata, 15.3% in A.thaliana, and 2.34% in A.halleri.
    • Observed distinct repeat amounts and compositions across different organs, tissues, and developmental stages, suggesting non-random distribution.

    Conclusions:

    • TRA 1.5 is a versatile tool for identifying various types of TRs in genomic and EST sequences.
    • The distribution of TRs in ESTs varies significantly among organs, tissues, and developmental stages.
    • Discovering TRs in ESTs provides valuable insights for gene mapping, association studies, and understanding gene function.