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

By William Walters, J. Gregory Caporaso, C. Lauber, Donna berg-Lyons, Noah Fierer, Rob Knight. Bioinform., 2011

386 citations recorded by the source corpus.

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 software available at http://pprospector.sourceforge.net Contact: rob.knight@colorado.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bd5d3fde2775bb50441f96285329b9b4c1d3135c

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Citations in the corpus

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs (2013, background): “has been optimized for broad coverage [46], such that it is nearly universal.”
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, methodology): “Software programs such as ecoPrimers (Riaz et al., 2011), ecoPCR (Ficetola et al., 2010), and PrimerProspector (Walters et al., 2011) can greatly assist in the design of barcode primers.”
Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys (2015, methodology): “The modified PCR and sequencing primers, including the Smith and Peay (2014) modified ITS sequencing primers and the bar-coded primer constructs (see Table S1 in the supplemental material) (http://www.earthmicrobiome.org/emp-standard-protocols/16s/; New Illumina HiSeq 16S primer sequences) were scre”
Specialized metabolic functions of keystone taxa sustain soil microbiome stability (2021, methodology): “The primers for the V4 hypervariable region of the bacterial 16S rRNA gene (515F: 5′-GTGCCAGC MGCCGCGGTAA-3′ and 806R: 5′-GGACTACHVG GGTWTCTAAT-3′) [36] were used to assess the composition and diversity of the incubated bacterial communities on an Illumina MiSeq instrument (300-bp pairedend reads).”
DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies (2014, background): “More recently, the program PrimerProspector was developed for design and evaluation of degenerate primers for taxonomic surveys (10).”