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Related Experiment Videos

TROLL--tandem repeat occurrence locator.

Adalberto T Castelo1, Wellington Martins, Guang R Gao

  • 1Department of Electrical and Computer Engineering, University of Delaware, 140 Evans Hall, NW 19716, USA. castelo@capsl.udel.edu

Bioinformatics (Oxford, England)
|May 23, 2002
PubMed
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Tandem Repeat Occurrence Locator (TROLL) efficiently identifies Simple Sequence Repeats (SSRs) using a modified Aho-Corasick algorithm. This fast, lightweight tool runs on standard personal computers, making genome-wide SSR analysis accessible.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Simple Sequence Repeats (SSRs) are crucial genetic markers.
  • Efficient identification of SSRs is essential for genomic studies.
  • Existing SSR finding tools may require substantial computational resources.

Purpose of the Study:

  • To develop a fast and lightweight tool for identifying SSRs.
  • To provide an accessible SSR detection method for standard personal computers.

Main Methods:

  • Implementation of the Tandem Repeat Occurrence Locator (TROLL) software.
  • Modification of the Aho-Corasick algorithm for SSR detection.
  • Utilizing a standard personal computer for analysis.

Main Results:

Related Experiment Videos

  • TROLL successfully identified all SSRs of length 20 bp or more on the Arabidopsis genome.
  • Analysis of the complete Arabidopsis genome (approx. 130 Mbases) was completed in 127 seconds.
  • The tool operated effectively on a PC Athlon 650 MHz with 256 MB of RAM.

Conclusions:

  • TROLL is a highly efficient and fast SSR finder.
  • The software is lightweight and requires only standard PC hardware.
  • TROLL offers a practical solution for genome-wide SSR analysis.