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 a

SUBMITTER: DeSantis TZ 

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

REPOSITORIES: biostudies-literature