TROLL--tandem repeat occurrence locator.
CONCLUSIONS
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.


BACKGROUND
TROLL is an open source project and is available at http://finder.sourceforge.net.
Castelo
Adalberto T
AT
Department of Electrical and Computer Engineering, University of Delaware, 140 Evans Hall, NW 19716, USA. castelo@capsl.udel.edu
Martins
Wellington
W
Gao
Guang R
GR
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D018745:Genome, Plant; D018895:Microsatellite Repeats / Q000235:genetics*; D010363:Pattern Recognition, Automated; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020080:Tandem Repeat Sequences / Q000235:genetics; D014584:User-Computer Interface