Dataset Information

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.

SUBMITTER: DeSantis TZ

PROVIDER: S-EPMC3097142 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

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Publications

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

DeSantis Todd Z TZ Keller Keith K Karaoz Ulas U Alekseyenko Alexander V AV Singh Navjeet N S NN Brodie Eoin L EL Pei Zhiheng Z Andersen Gary L GL Larsen Niels N

BMC ecology 20110427

<h4>Background</h4>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, ...[more]

PMID: 21524302

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Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

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