title: Simrank: Rapid and sensitive general-purpose k-mer search tool.
abstract: BACKGROUND
  Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available.
  
  
  RESULTS
  Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset.
  
  
  CONCLUSIONS
  Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.
authors.affiliation: Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, USA. tdesantis@lbl.gov
authors.forename: Todd Z
authors.initials: TZ
authors.lastname: DeSantis
authors.forename: Keith
authors.initials: K
authors.lastname: Keller
authors.forename: Ulas
authors.initials: U
authors.lastname: Karaoz
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Alekseyenko
authors.forename: Navjeet N S
authors.initials: NN
authors.lastname: Singh
authors.forename: Eoin L
authors.initials: EL
authors.lastname: Brodie
authors.forename: Zhiheng
authors.initials: Z
authors.lastname: Pei
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
authors.forename: Niels
authors.initials: N
authors.lastname: Larsen
mesh_terms: D019295:Computational Biology; D004247:DNA; D016206:Databases, Bibliographic; D016208:Databases, Factual; D008967:Molecular Biology; D011506:Proteins; D012313:RNA; D012984:Software
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA