There are many reasons to use Oligo. The first of which is the simple interface.
This is so simple that even a novice user can use it to design primers and probes using a built-in wizard.
When the user design primers, Oligo will automatically assess the quality of the primers by calculating the base pair composition, sequence homology, self-complementarity and self-dimerization. These features are used by Oligo’s Primer Analysis tool to generate a set of primers that cover your intended PCR region with good efficiency, but at the same time is not too large to hinder downstream reactions.
Another feature of Oligo is that it allows the user to use PCR primers and perform real time PCR. Oligo’s Primer Analysis tool takes the user through all the steps required to design primers for PCR.
Oligo will calculate a number of properties of a primer including melting temperature, amplicon size, Tm, GC%, amplicon pKa, dimerization free energy, stem free energy, loop size and Tm for DNA duplex.
In addition, the user can use the Primer Analysis Wizard, where they can quickly adjust settings such as base pair composition, base pair composition distribution, rate of the optimization and make all the settings saved automatically.
You can design multiple primer pairs in one file. Use the wizard to automate the process. With a few mouse clicks you can design primers for PCR, real time PCR, nucleic acid and protein sequencing, and molecular beacon.
Oligo supports a variety of thermodynamic data and the nearest neighbor thermodynamic data is the most up-to-date available.
In addition, Oligo supports Loop Denaturation, a thermodynamic model for designing loop primers. The “A-T loop” has been included. It is possible to design loop primers using this tool.
In addition, there is the Loop Stabilization tool, a new method to design loop primers. The “C-G” loop has been included.
Oligo will predict the dimerization of the designed primers. The dimerization free energy of the designed primers is also shown.
Oligo will predict the primer homology, i.e., the potential for primer-dimer formation.
With Oligo, you can easily design primers and other oligonucleotides for use in cloning, PCR and real-time PCR, 384a16bd22
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A keymacro is an optional key binding (that is, combination of keys) that is used to activate a DICT operation. You define a keymacro for each DICT operation that you perform, as shown below. You define the keymacro so that you can activate the DICT operation simply by pressing the key combination that you want to use. For instance, the following keymacro activates the get operation for the english dictionary.
DICTKEYMACRO KEYMACRO Example:
Set a keymacro for a DICT operation by creating a file with the keymacro in the keymacro file. To run a DICT operation using a keymacro, add the following line to your inetd.conf file:
Dict servers that support keymacro operations enable you to perform a DICT operation simply by pressing a key combination, rather than having to look up the keymacro name in the keymacro file.
KEYMACRO (Enhanced) Description:
As a special case, some DICT servers support the KEYMACRO (Enhanced) extension to the protocol. If the DICT server supports the enhanced mode, then you can activate a DICT operation using the following command:
where mymacro.pmh is a file containing the keymacro. If you use this enhanced mode of operation, then you can override the default keymacro behavior. You can define a keymacro (to activate a DICT operation) simply by pressing a key combination, as you can with a normal keymacro. For instance, the following keymacro activates the get operation for the english dictionary.
Dict servers that support the enhanced keymacro mode of operation enable you to perform a DICT operation simply by pressing a key combination, rather than having to look up the keymacro name in the keymacro file.
DICTKEYMACRO: KEYMACRO KEYMACRO KEYMACRO example:
You can use the #include feature to set a keymacro for a specific DICT operation. For example, you could set a keymacro for the get operation for the english dictionary by creating a file that includes the following line: