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primer design tools - primer designing (May/08/2002 )

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There are a number of programs at the following site:

Most are for special applications such as MSP, DGGE, SNP, in vitro translation etc. The oligo calculator is quite handy.


u can design your primer with genefisher,


QUOTE (kawaka @ Jan 23 2004, 11:03 AM)
What is the best online and free primer design tool?


I have gone through a free online primer analyzing tool, you can have a look:

This website offers another primer design software "Primer Premier" and its demo and time limited code can also be requested.
Thank you


Another free primer design tools for local installation

PerlPrimer - open-source PCR primer design

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.
PerlPrimer's current features include the following:

1. Calculation of possible primer-dimers
2. Retrieval of genomic or cdna sequences from Ensembl (including both sequences automatically for QPCR)
3. Ability to BLAST search primers using the NCBI server
4. Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.
5. ORF and CpG island detection algorithms
6. Ability to add cloning sequences to primers, automatically adjusted to be in-frame
QPCR primer design without manual intron-exon boundary entry

this is quite simple.


Here is another primer design program (free download at

"Fast PCR": a PCR primer design and repeat sequence searching programme with additional tools for the manipulation and analysis of DNA and protein

The program "Fast PCR" is based on the new approach in design PCR primers, alignment and repeat sequence searching. Program can work with several sequences simultaneously (up to 1,000,000), multiplex PCR primers design and "in silico" PCR is supported. The program is convenient for search homology in a personal database is similar to BLAST (the algorithm for the alignment of DNA sequences is based on a segment-to-segment alignment principle similar to DIALIGN) and also others bioinformatics tools are included. Powerful and fast search of all types of repeats in DNA based on the new theory of search of repeats is developed. Now the program supports clustering sequences.


QUOTE (rajgene @ Dec 27 2004, 07:29 AM)

This engine gives the same results as Primer3.


Here is a tool from Rutgers. It is offered for a price, but it gives you step by step instructions on primer design, and extensive documentation that incudes background information on PCR primers. There is also a free demo that can probably serve you.




Can Primer3 works with multiple sequences??


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