ArticleBMC ecology2011
Simrank: Rapid and sensitive general-purpose k-mer search tool.
Article in BMC ecology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed.
- Influence of Tributary Inflows on Sediment Bacterial Community Composition of the River Mainstem.Microorganisms · 2026Article
- Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base.PLoS computational biology · 2021Article
- Superstatistical model of bacterial DNA architecture.Scientific reports · 2017Article
- Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles.MicrobiologyOpen · 2015Article
- Probabilistic topic modeling for the analysis and classification of genomic sequences.BMC bioinformatics · 2015Article
- Article
- Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2014Article
- The Gut Microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity.BMC genomics · 2013Article
- Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.BMC bioinformatics · 2013Article
- Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs.PloS one · 2013Article
- Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.The ISME journal · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
backgroundTerabyte-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.
resultsHere 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.
conclusionsSimrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.