TROLL—Tandem Repeat Occurrence Locator | Zendy

Adalberto T. Castelo | Zendy; Wellington S. Martins | Zendy; Guang R. Gao | Zendy

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TROLL—Tandem Repeat Occurrence Locator

Author(s) -

Adalberto T. Castelo,

Wellington S. Martins,

Guang R. Gao

Publication year - 2002

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/18.4.634

Subject(s) - tandem , computer science , open source , tandem repeat , simple (philosophy) , microsatellite , sequence (biology) , net (polyhedron) , genome , software , computational biology , biology , operating system , genetics , mathematics , gene , engineering , philosophy , allele , geometry , epistemology , aerospace engineering

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.

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