Literature DB >> 12016062

TROLL--tandem repeat occurrence locator.

Adalberto T Castelo1, Wellington Martins, Guang R Gao.   

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.

Mesh：

Year:  2002        PMID： 12016062     DOI： 10.1093/bioinformatics/18.4.634

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  51 in total

1.  mreps: Efficient and flexible detection of tandem repeats in DNA.

Authors:  Roman Kolpakov; Ghizlane Bana; Gregory Kucherov
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

2.  ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval.

Authors:  Jeff Reneker; Chi-Ren Shyu; Peiyu Zeng; Joseph C Polacco; Walter Gassmann
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis.

Authors:  Niroj Kumar Sethy; Shalu Choudhary; Bhumika Shokeen; Sabhyata Bhatia
Journal:  Theor Appl Genet       Date:  2005-11-19       Impact factor: 5.699

4.  Development of chickpea EST-SSR markers and analysis of allelic variation across related species.

Authors:  Shalu Choudhary; Niroj Kumar Sethy; Bhumika Shokeen; Sabhyata Bhatia
Journal:  Theor Appl Genet       Date:  2008-11-20       Impact factor: 5.699

5.  Consensus higher order repeats and frequency of string distributions in human genome.

Authors:  Vladimir Paar; Ivan Basar; Marija Rosandić; Matko Gluncić
Journal:  Curr Genomics       Date:  2007-04       Impact factor: 2.236

6.  HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.

Authors:  Alexander Churbanov; Rachael Ryan; Nabeeh Hasan; Donovan Bailey; Haofeng Chen; Brook Milligan; Peter Houde
Journal:  Bioinformatics       Date:  2012-09-06       Impact factor: 6.937

7.  Searching microsatellites in DNA sequences: approaches used and tools developed.

Authors:  Atul Grover; Veenu Aishwarya; P C Sharma
Journal:  Physiol Mol Biol Plants       Date:  2011-12-23

8.  A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae).

Authors:  M C Moretzsohn; L Leoi; K Proite; P M Guimarães; S C M Leal-Bertioli; M A Gimenes; W S Martins; J F M Valls; D Grattapaglia; D J Bertioli
Journal:  Theor Appl Genet       Date:  2005-10-11       Impact factor: 5.699

9.  Identification and characterization of SSRs from soybean (Glycine max) ESTs.

Authors:  Dawei Xin; Jiaying Sun; Jialing Wang; Hongwei Jiang; Guohua Hu; Chunyan Liu; Qingshan Chen
Journal:  Mol Biol Rep       Date:  2012-06-29       Impact factor: 2.316

10.  A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome.

Authors:  Márcio C Moretzsohn; Andrea V G Barbosa; Dione M T Alves-Freitas; Cristiane Teixeira; Soraya C M Leal-Bertioli; Patrícia M Guimarães; Rinaldo W Pereira; Catalina R Lopes; Marcelo M Cavallari; José F M Valls; David J Bertioli; Marcos A Gimenes
Journal:  BMC Plant Biol       Date:  2009-04-07       Impact factor: 4.215
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