qPrimerDepot | Tool name | qPrimerDepot |
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| URL | http://primerdepot.nci.nih.gov/ |
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| Important features | 1. There are 3 unique sets of primers designed for 42,133 mouse and human RefSeq genes.
2. Over 90% of primers are designed bridging exon-exon junction.
3. Primers are designed such that they can be used for uniform annealing temperature of large high-throughput assays. |
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| Citations | Wenwu Cui, Dennis D Taub and Kevin Gardner: qPrimerDepot: a primer database for quantitative real time PCR. Nucleic Acids Research. 2006 Sep 29;35 (1):D805-D809. PubMed PMID:17068075 ; PubMed Central PMCID: PMC1635330 |
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| Year of publication | 2007 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | Junction primers, Real time PCR, Multiplexed PCR, Primer Database |
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| Category | Online, Free |
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| Features | 1. Database contains qRT-PCR primers for 99.96% of human refseq genes.
2. All the primer are designed to have uniform annealing temperature i.e. 60B0C.
3. More than 90% of primer pairs are designed from exon-exon junction.
4. Primers were designed using Primer3, length ranging 17-27 with 20 as optimum length, tm ranging between 57-63 with 60 as optimum.
5. BLAST was used to evaluate specificity of primer using Refseq database as reference and primer pairs with <80% identities were filtered out.
6. After in silico and experimental validation, it is concluded that 70-90% of the primer sets are likely to work without any changes in parameters. |
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| Description | |
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