PrimerProspector protocols

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PrimerProspector specifications

Information


Unique identifier OMICS_05884
Name PrimerProspector
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
PyCogent, Numpy, Matpolib
Maintained Yes

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Publication for PrimerProspector

PrimerProspector in pipelines

 (5)
2016
PMCID: 4865482
PMID: 27242686
DOI: 10.3389/fmicb.2016.00650

[…] all 16s rdna primers were queried using data from silva (klindworth et al., ; quast et al., ) and probebase (loy et al., )., to evaluate the primer-to-target 3′ mismatches, primers were tested with primerprospector 1.0.1 (walters et al., ) against the greengenes database (gg_13_5.fasta) containing 1,262,986 sequences (desantis et al., ). this database was curated using mothur (version 1.34.3) […]

2016
PMCID: 5118932
PMID: 27736792
DOI: 10.1128/AEM.02576-16

[…] 5.8s-fun would have wider coverage across fungi yet stronger selectivity, particularly against plants, than existing primers, including its3 (, ) and fits9 (). detailed taxonomic analyses with primerprospector support these expectations (; see also fig. s3 in the supplemental material). for example, fits9 will theoretically amplify all viridiplantae, as well as various algal and protist […]

2015
PMCID: 4374533
PMID: 25815185
DOI: 10.1186/s40168-015-0069-6

[…] classified as belonging to the taxon ck-1c4-19 were downloaded from the silva rrna database ssu ref web release 117 []. the v3-v4 region was extracted in silico from these 124 sequences using primerprospector v. 1.0.1 []. of the 124 sequences, 62 contained priming sites deemed likely to successfully amplify. examination of sequences predicted not to amplify revealed many misclassified […]

2015
PMCID: 4643231
PMID: 26563586
DOI: 10.1038/srep16498

[…] c. diphtheria, and s. pyogenes were retrieved from the comparative rna web site and project. to investigate the v3 and v4 regions of the 16s rrna gene, the silva ssu 111 database was queried using primerprospector v 1.0.1 and the primers u341f/534r (v3) and 515f/806r (v4), to retrieve the corresponding sequences. length distribution statistics were generated for the extracted v3 and v4 region […]

2012
PMCID: 3575276
PMID: 23009728
DOI: 10.1186/1471-2180-12-220

[…] were aligned using muscle v3.7 using default settings []., primer specificity was evaluated by scoring each primer sequence against the corresponding in silico generated target sequences using primerprospector []. to direct the scoring to the region where the primer sequence aligned for all strains, the primer region was extracted from the alignment and used alone as input to the scoring […]


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PrimerProspector in publications

 (18)
PMCID: 5729218
PMID: 29242834
DOI: 10.1128/mSphere.00488-17

[…] using mafft v7 (). of the 23,128 input sequences, some failed to align (n = 63) and were pruned from the input, and the entire set was realigned. the final aligned sequence set was then subjected to primerprospector () from the v1.9 release of qiime virtualbox () to obtain degenerate forward primers ()., reverse primers were created using the unite v7 database from the october 2014 release (). […]

PMCID: 5868293
PMID: 29102920
DOI: 10.1136/gutjnl-2017-314205

[…] and sequenced in an ion pgm torrent platform following manufacturer’s instructions. primers were designed following recommendations reported by andersson et al, and were extensively analysed using primerprospector (see online ). , the performance of the uparse pipeline was evaluated and compared with that reported for samples of the human microbiome project (hmp) data set. using uparse […]

PMCID: 5583490
PMID: 28733282
DOI: 10.1128/AEM.00806-17

[…] gene with no accompanying active bont gene cluster [e.g., within bont/a1(b)-producing organisms]. primers were developed to amplify the ntnh gene, and primer coverage was evaluated in silico with primerprospector by querying the primers against near-full-length ntnh genes extracted from genome assemblies. of the 138 near-full-length sequences analyzed, primerprospector predicted pcr […]

PMCID: 5468309
PMID: 28607435
DOI: 10.1038/s41598-017-03487-1

[…] in this case overlapping with the universal v4 reverse primer (figure )., the specificity of the 5′ and 3′ segments of all blocking primers was evaluated with the analyze_primers.py program of the primerprospector package against reference 18s rrna gene sequences from version 119 of the silva database. this program computes a local alignment for the input primer(s) against target sequences […]

PMCID: 5368227
PMID: 28400755
DOI: 10.3389/fmicb.2017.00494

[…] region, amplicon size, domain coverage rate and literature reference., primer position according to e. coli numbering (baker et al., ) umulative-sum-scal., primer pair coverage was calculated using primerprospector 1.0.1 according to the non-redundant silva ssu r123 database and the weighted score method (walters et al., )., the raw sequence data (sff-files) were pre-processed in qiime v1.9.1 […]


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PrimerProspector institution(s)
Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, CO, USA; Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA; Cooperative Institute for Research in Environmental Sciences, Boulder, CO, USA; Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Boulder, CO, USA
PrimerProspector funding source(s)
Bill and Melinda Gates foundation; Crohn's and Colitis foundation of America; Howard Hughes Medical Institute; National Institutes of Health Signaling and Cell Cycle Regulation Training Grant (T32GM008759)

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