PrimerSelect protocols

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PrimerSelect specifications

Information


Unique identifier OMICS_26646
Name PrimerSelect
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Maintained No

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Publication for PrimerSelect

PrimerSelect in pipelines

 (9)
2018
PMCID: 5819644
PMID: 29463303
DOI: 10.1186/s13104-018-3249-1

[…] penta- and hexanucleotides repeats were screened with the software msatcommander [, ] and sequences less than 100 bp and/or with a small number of repeats were excluded. primers were designed with primerselect software (part of the lasergene package []). every microsatellite sequence chosen was run through the online version of the basic local alignment search tool for nucleotide (blastn) [] […]

2018
PMCID: 5935750
PMID: 29728638
DOI: 10.1038/s41598-018-25514-5

[…] homology with other b. subtilis group strains were designated pcr targets. the specific primers used for b. velezensis and b. subtilis subsp. subtilis were generated using the dnastar lasergene primerselect module (version 7.0) (table ). primer synthesis was performed by the bioneer corporation (daejeon, korea). each primer set amplifies a specific dna fragment from only the targeted […]

2016
PMCID: 4777559
PMID: 26937960
DOI: 10.1371/journal.pone.0150485

[…] all pei candidate genes were amplified by pcr from genomic dna of cultivar ‘atlas’ (rrs2+, resistant) using specific forward and reverse primers (). primer development was done with the program primerselect™ which is part of the software suit dnastar® lasergene version 10 (dnastar, inc., madison, wisconsin, usa)., haplotype analysis and alignment of nucleotide sequences was performed […]

2012
PMCID: 3480386
PMID: 23112815
DOI: 10.1371/journal.pone.0047456

[…] on transcript (blastn) and protein (blastx) similarity searches using ncbi databases and gene specific primers designed to the resulting consensus sequences using dnastar lasergene® v8.0 software primerselect (usa)., to obtain 5′ regions for the acppc sequences amplified from the c3 est library a 22 nucleotide 5′ trans-spliced leader (sl) sequence , was used in combination with multiple gene […]

2011
PMCID: 3241691
PMID: 22194958
DOI: 10.1371/journal.pone.0028954

[…] bases were selected for the r. reniformis primer generation. these regions are divergent areas of dna sequence as described. the sequences were trimmed to the divergent areas and imported into primerselect® of the lasergene® software package. primer pairs were generated using primerselect®., the rr-β-tub primers () were evaluated in reactions having three different levels of dna sample […]


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PrimerSelect in publications

 (144)
PMCID: 5958096
PMID: 29773799
DOI: 10.1038/s41467-018-04398-z

[…] (qiagen, valencia, ca)., relative mrna abundance was determined using the sybr greener™ qpcr supermix system (invitrogen, carlsbad, ca). suitable amplification primers were designed using the primerselect tool of dnastar 14 software (madison, wi) or the ncbi online primer-blast program (supplementary table ). pcr reactions were performed in a volume of 10 μl containing 1 μl of diluted […]

PMCID: 5902611
PMID: 29662105
DOI: 10.1038/s41598-018-24541-6

[…] and l. plantarum subsp. argentoratensis, were evaluated and confirmed via two-step in-depth testing using the blast search engine (https://blast.ncbi.nlm.nih.gov/blast.cgi) and the lasergene primerselect program (version 7.2.1; dnastar inc., usa).table 1, in l. plantarum subsp. plantarum, the blastn searches presented no substantial match to known reference sequences […]

PMCID: 5906682
PMID: 29706902
DOI: 10.3389/fphys.2018.00380

[…] pcr detection system (bio rad), using perfecta qpcr fastmix ii (quantabio). primers listed in supplementary table were designed using primer3 server (version 4.0.0) (untergasser et al., ) or primerselect (dnastar), which amplify 107–247 bp fragments of cdna and amplification efficiency (e) was empirically verified to be 0.9–1.0. reactions were performed in 15 μl with 200 nm each primer […]

PMCID: 5897751
PMID: 29681895
DOI: 10.3389/fmicb.2018.00676

[…] putida dpa1 and also for the gyrb gene (used as reference gene in transcription analysis) were manually designed (supplementary table ) and checked for the formation of secondary structures by the primerselect™ program (lasergene®, dnastar). the specificity of each primer set was assessed in silico with the online tool primer-blast (http://www.ncbi.nlm.nih.gov/tools/primer-blast/) and by pcr […]

PMCID: 5766616
PMID: 29330432
DOI: 10.1038/s41598-017-18613-2

[…] microsatellites used in this study (see additional table ) were developed by us using a method described previously primers of each microsatellite were designed in the repeat-flanking regions using primerselect (dnastar, ca, usa). to genotype the microsartellites on the automatic dna sequencer abi3730xl (applied biosystems, foster city, ca, usa) one primer for each marker was labelled […]


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PrimerSelect institution(s)
Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, CA, USA
PrimerSelect funding source(s)
Supported by National Institutes of Health grants HG1736 and AI47400.

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