Bioinformatics. 2002 Apr;18(4):634-6.

TROLL--tandem repeat occurrence locator.

Source

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

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.

PMID:: 12016062; [PubMed - indexed for MEDLINE]

Free full text

Publication Types, MeSH Terms

Publication Types

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

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences. [Bioinformatics. 2006]
Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.
Mrázek J, Xie S. Bioinformatics. 2006 Dec 15; 22(24):3099-100. Epub 2006 Nov 8.
TRAP: automated classification, quantification and annotation of tandemly repeated sequences. [Bioinformatics. 2006]
TRAP: automated classification, quantification and annotation of tandemly repeated sequences.
Sobreira TJ, Durham AM, Gruber A. Bioinformatics. 2006 Feb 1; 22(3):361-2. Epub 2005 Dec 6.
Simple sequence repeat marker loci discovery using SSR primer. [Bioinformatics. 2004]
Simple sequence repeat marker loci discovery using SSR primer.
Robinson AJ, Love CG, Batley J, Barker G, Edwards D. Bioinformatics. 2004 Jun 12; 20(9):1475-6. Epub 2004 Feb 12.
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences. [Bioinformatics. 2004]
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences.
Bilgen M, Karaca M, Onus AN, Ince AG. Bioinformatics. 2004 Dec 12; 20(18):3379-86. Epub 2004 Jul 15.
Review Key-string algorithm--novel approach to computational analysis of repetitive sequences in human centromeric DNA. [Croat Med J. 2003]
Review Key-string algorithm--novel approach to computational analysis of repetitive sequences in human centromeric DNA.
Rosandić M, Paar V, Gluncić M, Basar I, Pavin N. Croat Med J. 2003 Aug; 44(4):386-406.

See reviews... See all...

Cited by 24 PubMed Central articles

Searching microsatellites in DNA sequences: approaches used and tools developed. [Physiol Mol Biol Plants. 2012]
Searching microsatellites in DNA sequences: approaches used and tools developed.
Grover A, Aishwarya V, Sharma PC. Physiol Mol Biol Plants. 2012 Jan; 18(1):11-9. Epub 2011 Dec 23.
Distribution and characterization of simple sequence repeats in Gossypium raimondii genome. [Bioinformation. 2012]
Distribution and characterization of simple sequence repeats in Gossypium raimondii genome.
Zou C, Lu C, Zhang Y, Song G. Bioinformation. 2012; 8(17):801-6. Epub 2012 Sep 11.
MsDetector: toward a standard computational tool for DNA microsatellites detection. [Nucleic Acids Res. 2013]
MsDetector: toward a standard computational tool for DNA microsatellites detection.
Girgis HZ, Sheetlin SL. Nucleic Acids Res. 2013 Jan 7; 41(1):e22. Epub 2012 Oct 2.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

TROLL--tandem repeat occurrence locator.
TROLL--tandem repeat occurrence locator.
Bioinformatics. 2002 Apr ;18(4):634-6.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: