TROLL--tandem repeat occurrence locator

Adalberto T Castelo; Wellington Martins; Guang R Gao

doi:10.1093/bioinformatics/18.4.634

TROLL--tandem repeat occurrence locator

Bioinformatics. 2002 Apr;18(4):634-6. doi: 10.1093/bioinformatics/18.4.634.

Authors

Adalberto T Castelo¹, Wellington Martins, Guang R Gao

Affiliation

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

PMID: 12016062
DOI: 10.1093/bioinformatics/18.4.634

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Arabidopsis / genetics
Genome, Plant*
Microsatellite Repeats / genetics*
Pattern Recognition, Automated
Sensitivity and Specificity
Sequence Analysis, DNA / methods*
Software*
Tandem Repeat Sequences / genetics
User-Computer Interface