Assay design tools for qPCR

IDT offers a group of free, online qPCR design tools to suit your specific application needs. Whether you want to quickly order a predesigned assay, or desire assistance with designing assays for a challenging target, IDT has a design tool that can help. With three different programs to choose from, it is important to know which will provide the optimal qPCR assay for your needs.

Each of the three design programs requires only the NCBI RefSeq number, which can be used to pull the target sequence from NCBI. If you are working with unannotated sequences, the freely available RealTime PCR and PrimerQuest® Tools can also design assays for a user-specified target.

Key features of assay design tools

PrimeTime® qPCR Predesigned qPCR Assay Database

  • Optimal design for human, mouse, and rat mRNA targets
  • Incorporates bioinformatics managing such factors as SNPs, BLAST searches to avoid cross-reaction and off-target amplification, and recognition of splice variants

RealTime PCR Tool

  • Designs specifically for qPCR, with some customization possible
  • Optimal design for targets that are not human, mouse, or rat
  • Can be used to effectively design assays for use with intercalating dyes such as SYBR® Green I (Molecular Probes, Inc.)

PrimerQuest® Tool

  • Highly customizable option for difficult qPCR designs

PrimeTime® Predesigned qPCR Assay Database

This program is designed to identify appropriate PrimeTime Predesigned qPCR Assays—assays that are predesigned, but not stocked. If your target is human, mouse, or rat, this program offers the highest level of bioinformatics analysis, including management of known SNPs, BLAST search to avoid cross reaction and off-target amplification, and recognition of splice variants. This database is regularly updated with current sequence information from NCBI, so it effectively designs assays with up-to-date bioinformatics. In this era of daily growth in genomic knowledge, having current sequence data is crucial.

Figure 1. The PrimeTime® Predesigned qPCR Assay Database instantly provides optimal assays for human, mouse, or rat.

RealTime PCR Tool

This program provides effective qPCR assay design through a user-friendly interface for targets other than human, mouse, and rat. This program allows for customization at many levels, including the ability to select the specific exon junctions to be targeted. For additional flexibility, the qPCR reaction conditions can be customized within this program, as well as the primer, probe, and amplicon parameters. If no customization is needed, this program can quickly draw on current NCBI data and recommend an assay for your qPCR target.

Figure 2. The RealTime PCR Tool allows for qPCR design and customization.

PrimerQuest® Tool

The PrimerQuest Tool is a useful program for PCR assay designs with non-standard requirements. This program is not specific for qPCR design like our other two programs, but if your design requires more demanding customization, this highly flexible program can be of great use. PrimerQuest designs can be customized in many ways, such as directing the assay towards certain areas of your target or by specifying primer or probe sequences. IDT Technical Support can also offer assistance with this program to help you meet your specific design challenges.Contact them at

Figure 3. Some of the qPCR parameters customizable with the highly flexible PrimerQuest® Tool.


  1. 17 Wedge 19 May
    A comprehensive discussion of the legal considerations for a web design business is beyond the scope of this article but many resources are available to provide more information about this topic (both online and in print). page; be sure to include a site map, partly because it makes the browsing experience for your customers more smooth, efficient, and less of a hassle, but primarily because a site map is an excellent way of improving your search engine optimisation results. Search Engine Optimization: Create use of effective search engine optimization processes to form positive that your web site well optimized, so it ranks well in search engine results.
  2. 16 Hatfield 19 May
    Take control of your next website design project and experience the freedom of creativity. Visitors are more likely to spend time with and return to a website that looks attractive. Hiring a local web design company has various benefits.
  3. 15 Wyselaskie 19 May
    Take control of your next website design project and experience the freedom of creativity. There are quite a few site building tools you can use but not a lot of them work when you consider the personal visions you have. Sandvox supports Google integration including Google Analytics and Google Webmaster Tools.
  4. 14 Prater 19 May
    I think this is one of the most vital information for me. And i am glad reading your article. But wanna remark on few general things, The web site style is wonderful, the articles is really excellent : D. Good job, cheers
  5. 13 Chapa 21 May
    s no single ɡreater influence on youг health tҺan the food you eat ѕeveral times a day, eνery single day օf your life. TҺe right waʏ is aƅout planning іn advance to give not only energy bսt nutrition. ӏ alsο recommend periodically monitoring aand recording ʏour bloold pressure.
  6. 12 Ridenour 21 May
    Elevated production օf lactic acid or illnesses thɑt ѕtοp thе elimination of the acid can result in metabolic acidosis, іn accorԀance wіth Medline - Ƥlus. Ƭhe right way is aboht planning іn dvance to give not оnly energy Ьut nutrition. Ӏ also recommend periodically monitoring аnd recording yоur blood pressure.
  7. 11 Lakeland 23 May
    Тhese energy supplements сontain Ƅoth natural ɑnd synthetic ingredients. Ѕo find out more aand catch mօre big fish on cheap thermogenic homemade baits annd ground baits аnd implrove your options for life. TҺе purpose аnd objective of tɦе study summarized at tthe site notes tɦаt thе objective of that rеsearch iѕ: "An initial preliminary, open label pilot study demonstrated a positive benefit of D-ribose in 'Baby-Boomer' subjects aged 50 to 65 years old complaining of persistent fatigue.
  8. 10 Fuller 23 May
    For instance, anaerobic exercise սses onlү glucose, wheгeas aerobic exercise սseѕ all three fuels. By uѕing Advo - Care products, ʏοu ϲan see the difference it maҡеs in уoսr sports life. Nuts ɑnd seeds Һelp yoսr energy bү suppressing thе աant to feel hungry.
  9. 9 Schulz 23 May
    I dο trust ɑll tɦe ideas yoս have introduced on your post. They're reаlly convincing and ϲan cеrtainly work. Nonetheless, thе posts aгe very short for newbies. Ӎay juѕt үoս ρlease extend thеm а bit from subsequent time? Thank уоu fоr tɦe post.
  10. 8 Cottle 30 May
    You're so cool! I don't believe I have read through anything like this before. So nice to discover another person with unique thoughts on this subject matter. Seriously.. many thanks for starting this up. This site is something that's needed on the web, someone with some originality!
  11. 7 Babcock 31 May
    I'd like to find out more? I'd care to find out some additional information.
  12. 6 Bladin 03 Jun
    Hey, you used to write fantastic, but the last several posts have been kinda boringˇK I miss your great writings. Past several posts are just a little out of track! come on!
  13. 5 List 04 Jun
    That is a good tip particularly to those fresh to the blogosphere. Brief but very accurate information… Many thanks for sharing this one. A must read post!
  14. 4 Birtwistle 05 Jun
    hi!,I really like your writing so much! proportion we keep in touch extra about your article on AOL? I need an expert in this house to resolve my problem. May be that is you! Having a look ahead to see you.
  15. 3 Hearn 08 Jun
    Nicce post. I learn something new and challenging on sites I stumbleupon everyday. It will always bee helpful tto read content from other authors andd use a little something fom their sites.
  16. 2 Brindley 15 Jun
    It's wonderful that youu are getting ideas from this article as well as from ourr argument made at this place.
  17. 1 Lenehan 17 Jun
    Can you tell us more about this? I'd care to find out more details.


Get a free, ongoing print or email subscription to the DECODED newsletter by registering online.