Search for Primers & Probes
OLIGO's primer search is the most comprehensive primer search ever devised for PCR. Users may customize their search to account for the following parameters: 3' dimers and 3' hairpins (measured by both structure and stability), primer and product lengths, 3' terminal stability, GC clamps, false priming (in the template and in other sequence files), homooligomers/sequence repeats, repeptitive elements by species, frequency of occurance by species, cross-compatibility (dimers), as well as compatible melting temperatures and priming efficiencies of selected primers. Next to each search option in the "Search for Primers and Probes" dialog box is a button to activate or deactivate that search option. When a button is activated, the individual subsearches that are components of the search are indicated by checked boxes. The Search Ranges dialog box and Search Parameters dialog box may be accessed by clicking on the respective buttons in the "Search for Primers and Probes" dialog box.
The "Search Parameters" dialog box is accessed by clicking on the "Parameters" button on the "Search for Primers and Probes" dialog box. It contains the program default selection limits (parameters) for the various subsearches used by OLIGO's automated (composite) searches. It is also the only place in the program where you can customize a given search (or subsearch) by entering a search setting different than the default value, and locking this value (from automatic stringency changes). The "Search Stringency" button provides you with the ability to change globally all search parameters in discrete increments preset in the OLIGO program using a single operation: YOU DON'T NEED TO KNOW how to change various parameters.