QuantPrime – a flexible tool for reliable high-throughput primer design for quantitative PCR

BMC Bioinformatics

Table 1 Examples of transcriptome annotations available on the public QuantPrime server

	Annotated features included in QuantPrime
Species	Genomic sequences	Splice variants	Keyword search	Annotation source	Reference
254 different species or crosses	No	No	Yes	TIGR plant transcript assemblies	[22]
91 different species or crosses	No	No	Yes	UniGene	[23]
Arabidopsis thaliana	Yes	Yes	Yes	TAIR release 7	[24]
Aspergillus niger	Yes	No	No*	JGI assembly v1.0	Non-published data
Bos taurus	Yes	No	Yes	NCBI RefSeq	[25]
Chlamydomonas reinhardtii	Yes	No	No*	JGI assembly v3.1	[26]
Danio rerio	Yes	No	Yes	NCBI RefSeq	[25]
Drosophila melanogaster	Yes	Yes	Yes	FlyBase release 5.4	[27]
Homo sapiens	Yes	No	Yes	NCBI RefSeq	[25]
Homo sapiens	Yes	Yes	Yes	H-Invitational Database 5.0	[28]
Mus musculus	Yes	No	Yes	NCBI RefSeq	[25]
Oryza sativa ssp japonica	Yes	Yes	Yes	TIGR release 5	[29]
Ostreococcus lucimarinus	Yes	No	No*	JGI assembly v2.0	Non-published data
Physcomitrella patens ssp patens	Yes	No	No*	JGI assembly v1.1	[30]
Populus trichocarpa	Yes	No	No*	JGI assembly v1.1	[31]
Rattus norvegicus	Yes	No	Yes	NCBI RefSeq	[25]
Saccharomyces cerevisiae	Yes	No	Yes	Saccharomyces Genome Database	[32]
Selaginella moellendorffii	Yes	No	No*	JGI assembly v1.0	Non-published data
Vitis vinifera	Yes	No	No	Genoscope assembly	[33]
Xenopus tropicalis	Yes	No	Yes	NCBI RefSeq	[25]

The latest versions of the annotations were added, and are updated regularly as updates become available.
* Protein IDs are searchable.

ISSN: 1471-2105