Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: https://gecftools.epfl.ch/getprime
Full name: Gene and Transcript-specific Primer Database
Description: GETPrime is a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design.
Year founded: 2011
Last update: 2015-11-12
Version: v 2.0
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Switzerland
Data type:
DNA
Data object:
Database category:
Major organism:
Keywords:

Contact information

University/Institution: Ecole Polytechnique Fédérale de Lausanne, Institute of Bioengineering
Address: Station 15,1015 Lausanne,Switzerland
City: Lausanne
Province/State:
Country/Region: Switzerland
Contact name (PI/Team): Bart Deplancke
Contact email (PI/Helpdesk): bart.deplancke@epfl.ch

Publications

28053161
GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms. [PMID: 28053161]
David FP, Rougemont J, Deplancke B.

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing gene- and transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification of one or several splice variants of most known genes. To ease selection, primers have also been ranked according to defined criteria such as genome-wide specificity (with BLAST), amplicon size, and isoform coverage. Here, we report a major upgrade (2.0) of the database: eight new species (yeast, chicken, macaque, chimpanzee, rat, platypus, pufferfish, and Anolis carolinensis) now complement the five already included in the previous version (human, mouse, zebrafish, fly, and worm). Furthermore, the genomic reference has been updated to Ensembl v81 (while keeping earlier versions for backward compatibility) as a result of re-designing the back-end database and automating the import of relevant sections of the Ensembl database in species-independent fashion. This also allowed us to map known polymorphisms to the primers (on average three per primer for human), with the aim of reducing experimental error when targeting specific strains or individuals. Another consequence is that the inclusion of future Ensembl releases and other species has now become a relatively straightforward task. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2017:45(D1) | 8 Citations (from Europe PMC, 2021-06-19)
21917859
GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR. [PMID: 21917859]
Gubelmann C, Gattiker A, Massouras A, Hens K, David F, Decouttere F, Rougemont J, Deplancke B.

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch.

Database (Oxford). 2011:2011() | 26 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
1986/5061 (60.779%)
Expression:
389/924 (58.009%)
1986
Total Rank
34
Citations
3.4
z-index

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Record metadata

Created on: 2015-06-20
Curated by:
[2018-11-29]
Shixiang Sun [2017-02-13]
Shixiang Sun [2017-02-08]
lin liu [2016-03-29]
lin liu [2016-03-26]
Jian Sang [2015-12-05]
Jian Sang [2015-06-28]