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DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences
ABSTRACT DECIPHER is a new method for finding 16S rRNA chimeric sequences by the use of a search-based approach. The method is based upon detecting short fragments that are uncommon in theExpand
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Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R
In recent years, the cost of DNA sequencing has decreased at a rate that has outpaced improvements in memory capacity. It is now common to collect or have access to many gigabytes of biologicalExpand
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Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates.
We describe a semi-empirical framework that combines thermodynamic models of primer hybridization with experimentally determined elongation biases introduced by 3'-end mismatches for improvingExpand
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Quality filtering of Illumina index reads mitigates sample cross-talk
BackgroundMultiplexing multiple samples during Illumina sequencing is a common practice and is rapidly growing in importance as the throughput of the platform increases. Misassignments duringExpand
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Inhibitory interactions promote frequent bistability among competing bacteria
It is largely unknown how the process of microbial community assembly is affected by the order of species arrival, initial species abundances and interactions between species. A minimal way ofExpand
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Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for Accurate Identification
ABSTRACT Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as anExpand
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Stochastic exits from dormancy give rise to heavy-tailed distributions of descendants in bacterial populations
Variance in reproductive success is a major determinant of the degree of genetic drift in a population. While many plants and animals exhibit high variance in their number of progeny, far less isExpand
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Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics
Application of high-density microarrays to the diagnostic analysis of microbial communities is challenged by the optimization of oligonucleotide probe sensitivity and specificity, as it is generallyExpand
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Mathematical tools to optimize the design of oligonucleotide probes and primers
The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity andExpand
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The Art of Multiple Sequence Alignment in R
Figure 1: The art of multiple sequence alignment. This document is intended to illustrate the art of multiple sequence alignment in R using DECIPHER. Even though its beauty is often concealed,Expand
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