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PRIMEGENS specifications


Unique identifier OMICS_00637
Alternative name PRIMEGENSw3
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes



Unique identifier OMICS_00637
Alternative name PRIMEGENSw3
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL
Maintained Yes




No version available


Publications for PRIMEGENS

PRIMEGENS citations


Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease in Lagerstroemia indica

Int J Genomics
PMCID: 4515301
PMID: 26247009
DOI: 10.1155/2015/528395

[…] ed and quantified using the Nanodrop (ND-1000) spectrophotometer (Nanodrop products, Wilmington, DE). Twenty-one primer pairs from differential expressed candidate genes were designed using an online PRIMEGENS program ( and synthesized from IDT Technologies (Integrated DNA Technologies, Coralville, IA). The working stock of each primer was adjusted to 2 μM. The gene IDs and p […]


Genome wide expression analysis of soybean NF Y genes reveals potential function in development and drought response

Mol Genet Genomics
PMCID: 4435856
PMID: 25542200
DOI: 10.1007/s00438-014-0978-2

[…] ript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA) in a reaction volume of 20 µL. Quantitative real-time PCR (qRT-PCR) was performed to quantify mRNA expression under drought conditions. Initially, PRIMEGENS (Srivastava and Xu ) was used to design primers for soybean NF-Y gene family and all the obtained sequences were manually verified for specific alignment by Blast against the soybean genome […]


Enhancement of immunogenicity and efficacy of a plasmid DNA rabies vaccine by nanoformulation with a fourth generation amine terminated poly(ether imine) dendrimer

PMCID: 3912024
PMID: 24501540
DOI: 10.2147/IJN.S53415

[…] ) and EcoRI (catalog number R0101S) were purchased from New England BioLabs Ltd. (Ipswich, MA, USA). The primers used in the study were designed using nucleotide sequences available in GenBank, using PRIMEGENS v2.0.5 software (Digital Biology Laboratory, University of Missouri-Columbia, Columbia, MO, USA), and synthesized at Eurofins Genomics India Pvt Ltd., Bangalore, India. […]


A Toolkit for bulk PCR based marker design from next generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

BMC Genomics
PMCID: 3534495
PMID: 23157543
DOI: 10.1186/1471-2164-13-637

[…] ipts’ without code or detail sufficient to permit reproducibility by non-specialists. Web-based tools suitable for larger-scale primer design include SNP-RFLPing [] for mammalian SNP assay design and PRIMEGENS-w3 [] which provides a variety of options for assay and probe design, especially for well-characterized genomes. Neither of these tools provides source code and the web-based tools they prov […]


Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

Nucleic Acids Res
PMCID: 3201883
PMID: 21785137
DOI: 10.1093/nar/gkr598

[…] ithin a given CGI across the genome. CGIs <500 bp only have one probe per island; (ii) one capture probe per transcription start sites (TSS) for all RefSeq genes. We implemented these criteria in the PRIMEGENS-v2 software to search for unique 160-bp segments within the targeted regions (,). A highly stringent criterion for cross hybridization was used and only highly specific probes were selected. […]


Generation and Validation of a Shewanella oneidensis MR 1 Clone Set for Protein Expression and Phage Display

PLoS One
PMCID: 2500165
PMID: 18714347
DOI: 10.1371/journal.pone.0002983

[…] l peptides were determined using Signal-P prediction ( and the corresponding encoding DNA sequences were removed prior to primer design. Further analysis using PRIMEGENS was performed to identify repetitive ORFs, for which one pair of primers was designed for a group . In total, 4526 unique pairs of primers were designed for S. oneidensis. The general guidel […]


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PRIMEGENS institution(s)
Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
PRIMEGENS funding source(s)
Supported by National Institute of Health (Grant 1R01-DA025779), the Congressionally Directed Medical Research Programs, U.S. Army Medical Research and Materiel Command (Grant BC062135), and in part by the Paul K. and Diane Shumaker Endowment in Bioinformatics.


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