Bioinformatics Vol. 18 no. 4 2002
Pages 634-636
© 2002 Oxford University Press
Applications Note |
TROLL—Tandem Repeat Occurrence Locator
Department of Electrical and Computer Engineering, University of Delaware, 140 Evans Hall, NW 19716, USA
Received on June 29, 2001
; revised on November 30, 2001
; accepted on December 6, 2001
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.
Contact: castelo{at}capsl.udel.edu
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