PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

@article{Walters2011PrimerProspectorDN,
  title={PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers},
  author={William A. Walters and J. Gregory Caporaso and Christian L. Lauber and Donna Berg-Lyons and Noah Fierer and Rob Knight},
  journal={Bioinformatics},
  year={2011},
  volume={27},
  pages={1159 - 1161}
}
Motivation: PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task. Results: PrimerProspector is an open-source software package that allows researchers to develop new primers from collections of sequences and to evaluate existing primers in the context of taxonomic data. Availability: PrimerProspector is open-source… 

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References

SHOWING 1-10 OF 13 REFERENCES
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing
TLDR
The functions implemented by barcrawl and bartab are described and a proof-of-concept case study of both programs in which barcoded rRNA primers were designed and validated by high-throughput sequencing are presented.
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
TLDR
Using error-correcting DNA barcodes, one run of a massively parallel pyrosequencer is constructed that characterized nearly as many 16S rRNA genes as have been sequenced to date by Sanger sequencing.
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
TLDR
There is incongruent taxonomic nomenclature among curators even at the phylum level, and environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic
PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database.
TLDR
PRIMROSE is a computer program for identifying 16S rRNA probes and PCR primers for use as phylogenetic and ecological tools in the identification and enumeration of bacteria and a comparison with PROBE DESIGN within the ARB software package shows that PRIMRose is capable of identifying oligonucleotides with a higher specificity.
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
TLDR
This work uses three large 16S rRNA datasets to test whether taxonomic information based on the full-length sequences can be recaptured by short reads that simulate the pyrosequencer outputs, and finds that different taxonomic assignment methods vary radically in their ability to recapture the taxonomic Information.
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
TLDR
This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
A renaissance for the pioneering 16S rRNA gene.
Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
TLDR
The RDP Classifier can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes, and the majority of the classification errors appear to be due to anomalies in the current taxonomies.
PyCogent: a toolkit for making sense from sequence
TLDR
The COmparative GENomic Toolkit is implemented in Python, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.
...
...