title: GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms.
abstract: 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.
authors.affiliation: Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.|Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
authors.forename: Fabrice P A
authors.initials: FP
authors.lastname: David
authors.affiliation: Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland bart.deplancke@epfl.ch.|Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.affiliation: Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland Jacques.rougemont@epfl.ch.|Laboratory of Systems Biology and Genetics, Institute of Bio-engineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
authors.forename: Bart
authors.initials: B
authors.lastname: Deplancke
mesh_terms: D000818:Animals; D017931:DNA Primers; D030561:Databases, Nucleic Acid; D005796:Genes; D006801:Humans; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D012313:RNA / Q000737:chemistry; D051381:Rats; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D017931:DNA Primers; D012313:RNA