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BMC Ecol. 2011 Apr 27;11:11. doi: 10.1186/1472-6785-11-11.

Simrank: Rapid and sensitive general-purpose k-mer search tool.

Author information

1
Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, USA. tdesantis@lbl.gov

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.

PMID:
21524302
PMCID:
PMC3097142
DOI:
10.1186/1472-6785-11-11
[Indexed for MEDLINE]
Free PMC Article
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