TROLL — Tandem Repeat Occurrence Locator. Summary: Tandem Repeat Occurrence Locator (TROLL), is a light-weight Simple Sequence Repeat (SSR) finder based on a slight modification of the Aho–Corasick algorithm. It is fast and only requires a standard Personal Computer (PC) to operate. We report running times of 127 s to find all SSRs of length 20 bp or more on the complete Arabdopsis genome—approx. 130 Mbases divided in five chromosomes—using a PC Athlon 650 MHz with 256 MB of RAM. Availability: TROLL is an open source project and is available at http://finder.sourceforge.net.
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References in zbMATH (referenced in 3 articles )
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- de Ridder, C.; Kourie, D.G.; Watson, B.W.; Fourie, T.R.; Reyneke, P.V.: Fine-tuning the search for microsatellites (2013)
- Chaley, Maria; Kutyrkin, Vladimir: Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences (2008)
- Leung, H.F.; Peng, Z.S.; Ting, H.F.: An efficient algorithm for online square detection (2006)