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Related Experiment Videos

Exact tandem repeats analyzer (E-TRA): a new program for DNA sequence mining.

Mehmet Karaca1, Mehmet Bilgen, A Naci Onus

  • 1Faculty of Agriculture, Akdeniz University, 07059 Antalya, Turkey. mkaraca@akdeniz.edu.tr

Journal of Genetics
|May 7, 2005
PubMed
Summary

Exact Tandem Repeats Analyzer 1.0 (E-TRA) identifies simple and non-simple tandem repeats in DNA sequences. This tool reveals that human tissues and developmental stages show non-random repeat distribution, aiding genetic studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Tandem repeats (TRs) are DNA sequences found in prokaryotes and eukaryotes.
  • Some TRs regulate gene expression, while others have unknown functions.
  • TRs are valuable in DNA profiling and genetic linkage analysis.

Purpose of the Study:

  • To introduce Exact Tandem Repeats Analyzer 1.0 (E-TRA), a novel tool for identifying simple and non-simple tandem repeats.
  • To analyze the distribution and composition of expressed tandem repeats in human EST sequences.
  • To compare repeat patterns across different human organs, tissues, cell lines, and developmental stages.

Main Methods:

  • E-TRA analyzes GenBank, FASTA, and expressed sequence tag (EST) files, supporting multiple file and sequence analysis.

Related Experiment Videos

  • The tool allows for user-defined parameters, including minimum and maximum motif lengths (1-1000 bp) and simultaneous search criteria.
  • A large dataset of 5,465,605 human EST sequences from 18,814,550 GenBank EST sequences was analyzed.

    • Main Results:

    • E-TRA identified simple and non-simple repeat string patterns in 12.44% (679,800) of the analyzed human EST sequences.
    • Repeat lengths varied from one to 126 nucleotides.
    • Significant differences in repeat number and composition were observed across human organs, tissues, cell lines, and developmental stages.

    Conclusions:

    • The distribution of expressed tandem repeats in human tissues and organs is not random.
    • E-TRA provides advanced capabilities for analyzing tandem repeats in diverse sequence data.
    • Findings suggest tissue-specific roles or regulation influenced by tandem repeat composition.