Oligo Explorer is a powerful tool to search PCR primers and primer pairs, analyzes all important primer properties like Tm, GC%, primer loops, primer dimers and etc. You can select primers manually form the sequence. Oligo Explorer includes also a powerful tool named Primer wizard that helps you to find suitable primer pairs for your purposes.

You can set your own parameters for primer pair search engine or use default parameters. Default parameters are usually adequate for most applications. Primer wizard suggests primer pairs that amplify PCR-product of given length. Individual primer pairs have been tested so that they do not form stable primer dimers or primer loops.

Oligo Explorer should be simple and self explanatory.

All you need to select primer manually is mouse. Use mouse buttons to select primers 3'-end from the 'Tm graph' page.

To do primer selection automaticly you can use "Primer search" that efficiently search primer pairs that meet all the requirements you specify. You can set your own parameters for primer pair search engine or use default parameters. You can find all the setting on 'Setting' page. Default parameters are usually adequate for most applications. "Primer search" suggests primer pairs that amplify PCR-product of given length. Individual primer pairs have been tested so that they do not form stable primer dimers or primer loops.

See the screenshot picture below to get some kind of idea from Oligo Explorer.
1. The picture below represents 'Tm graph' window of the current sequence. Melting temperature (Tm) graph reveal a primer melting temperature (The primer whose 3'-end is in given position and lengt specified on the tool bar).
* Primers could be selected using mouse buttons. Left mouse button select Upper primer and rigth mouse button select lower primer. Bushing the mouse button you select 3'-end position for the primer.
* Immediately after you have selected primer you can easily see all the important properties of the primer on the bottom of the current window. Right panel illustrate thermodynamical properties and left panel show all the possible loop formations.

2. For the 'Primer search' you are allowed to determine search parameters the best suit for you purposes.
* When you have made your changes to parameters you have to push the 'Search' button and wait a few seconds.
* "Reset" button resets your parameters to the defaults (These are the defaults that you have defined through the "Options dialog")
* "Defaults" button resets parameters to the "Oligo Explorer defaults" (Your are not able to change these default settings)
* "Advanced..." button opens the "Advanced options dialog". Through this dialog you are able to choose repeat filtering and primer uniqueness search settings.
* "Search log..." allows you to browse through primer search progress. There you will find detailed information gathered during primer pair searching.

3. Immediately after search operation 'Oligo Explorer' show the list of the suitable primer pairs. All the primer pairs on the list meet the requirements you spcified on on setting page.
Immediately after you have selected primer from the list you can easily see all the important properties of the primer pair on the bottom of the current window. Right panel illustrate thermodynamical properties and left panel show all the possible loop formations.

4. Finally you can save the results in the file in txt or rtf format. You can also print results using "Print preview" dialog.

Please Note: this program is free for academic use only.

The license of this software is Freeware, you can free download and free use this calculator software.