You can try with Gene Runner software version 3.01 . I'm using it and quite good. You can cross-check the primers with every possible difficulties that might hamper your expt later with the help of this software!! But, yes, the software is compatible for Windows 7 (32 bits) not for 64 bits.

http://www.generunner.net/

Try Primer3Plus http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi/ IT IS VERY GOOD ONLINE TOOL FOR PRIMER DESIGNING

Thank you very much, Dr. Sanjay.

http://www.ncbi.nlm.nih.gov/tools/primer-blast/ I have used this to successfully design primers for both standard and qPCR

Primer3 is best suited to design almost all types of primers. To validate further, blast the designed sequences to get perfect hit. For qRT-PCR, try http://eu.idtdna.com/pages/scitools

I have been using these tools for many years.

Vinita Pachauri

[email protected]

ncbi is better as it BLAST the designed primers so as to confirm mismatch if any

Thank you very much, Dr. Sara, Dr. Vinita and Dr. Sanjay.

Thank you, Dr. Chan. It appears very interesting. I am going to learn more about it.

The Sigma website for primer design uses Beacon Designer to generate your primers. In my opinion Beacon Designer (and its sibling Allele ID) are the most consistent and best primer design programmes for qPCR/RT-qPCR. Unfortunately they are expensive to buy for an individual researcher, so having access to the programme through Sigma's website is really useful. If need be, Sigma will also help you with your designs.

http://www.sigmaaldrich.com/life-science/custom-oligos/dna-probes/product-lines/probe-design-services/oligoarchitect-online.html

Thanks a lot, Dr. Stephen.

Try Primer3Plus http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi/ IT

Dear,

it is pretty good you go with primer3 tool, it is best one in all parameter of a good primer designing but if you want manually you can use oligocaculator of just-bio where you can designed primers of your will according to all requirement of primer designing like GC content, annealing temperature and to remove repetitive G or C at 3-end, hope its work for you

be happy

You can try with Gene Runner software version 3.01 . I'm using it and quite good. You can cross-check the primers with every possible difficulties that might hamper your expt later with the help of this software!! But, yes, the software is compatible for Windows 7 (32 bits) not for 64 bits.

http://www.generunner.net/

Thanks a lot, Mr. Debaprasad. I found it compatible with my Windows system. It is really interesting and with a wide range of functions, including those pertaining to restriction enzymes. Pleased that it is free.

Kind regards!

Best of Luck Dr. Rashad !!

geneTool, primer3

Why don't you try PrimerBlast available on NCBI website? It's a mix of Primer3 and blast to check the potential amplification of off-target transcripts, quite usefull for RT-qPCR...!

Good luck!

Hi, Though there are so many online tools available, I have used the Oligo explorer offline tool for primer design. Its a direct and very simple tool, where you can manually play with the sequence and get the right combination of primers with the desired properties. You can register and download the software from the link: http://www.genelink.com/tools/gl-oe.asp

Ncbi primer blast - defenitely fast and easy and you safe yourself the time to go back and blast against possible unintended targets... Worked fine for me.

Oh... Just realized oliver suggested the same... ;)

Thank you all.

There are number of tools for primer designing like

primer3, ncbi blast, prime select tool,

idt tool, etc.

Use oligos , dnaman or bioedit software (offline tools)

which one is the easiest for novice? I want to design guessmers for bacterial lipases which have not been sequenced before. 

you can also download Beacon Designer, it is easy to use Rashad Abdul-Ghani