title: WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures.
abstract: BACKGROUND
  An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements (called words or motifs). Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets.
  
  
  METHODS
  This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA word space and (2) scores words with a distributed Markov chain model.
  
  
  RESULTS
  A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of Arabidopsis thaliana; the results of the analysis were integrated into The Arabidopsis Gene Regulatory Information Server (AGRIS). A public version of WordSeeker was deployed on the Glenn cluster at the Ohio Supercomputer Center.
  
  
  CONCLUSIONS
  WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data.
authors.affiliation: Bioinformatics Laboratory, School of EECS, Ohio University, Athens, Ohio 45701, USA. lichtenj@ohio.edu
authors.forename: Jens
authors.initials: J
authors.lastname: Lichtenberg
authors.forename: Kyle
authors.initials: K
authors.lastname: Kurz
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Liang
authors.forename: Rami
authors.initials: R
authors.lastname: Al-ouran
authors.forename: Lev
authors.initials: L
authors.lastname: Neiman
authors.forename: Lee J
authors.initials: LJ
authors.lastname: Nau
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Welch
authors.forename: Edwin
authors.initials: E
authors.lastname: Jacox
authors.forename: Thomas
authors.initials: T
authors.lastname: Bitterman
authors.forename: Klaus
authors.initials: K
authors.lastname: Ecker
authors.forename: Laura
authors.initials: L
authors.lastname: Elnitski
authors.forename: Frank
authors.initials: F
authors.lastname: Drews
authors.forename: Stephen Sauchi
authors.initials: SS
authors.lastname: Lee
authors.forename: Lonnie R
authors.initials: LR
authors.lastname: Welch
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D004247:DNA / Q000737:chemistry*; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D008390:Markov Chains; D012045:Regulatory Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004247:DNA