Group-specific (family-specific primer set) and Unique PCR primers design

Group-specific amplification, also call family-specific and sequence-specific amplification, is an important tool for comparative studies of related genes, sequences and genomes that can be applied to studies of evolution, especially for gene families and for cloning new related sequences.
Specific targets such as homologous genes or members of a transposable element family can be amplified to uncover DNA polymorphisms associated with these sequences or other genetic investigations. The overall strategy of designing group-specific PCR primers uses a hash index of 12-mers to identify common regions in the target sequences, followed by standard PCR primer design for the current sequence, and then testing of complementarity of these primers to the other sequences. FastPCR performs sequences multiple alignment or does accept alignment sequences input, giving it the flexibility to use a different strategy for primer design. If required, it can design degenerate PCR primers to amplify the polymorphic region of all related sequences.
The FastPCR package designs large sets of universal primer pairs for each given sequence, identifies conserved regions, and generates suitable primers for all given targets. The steps of the algorithm are performed automatically and the user can influence the settings for the primer design options. The quality of primer design is dependent on sequence relationships, genetic similarity, and suitability of the consensus sequence for the design of good primers.
The software is able to generate group-specific primers for each set of sequences independently, which are suitable for all sequences. Primer alignment parameters for group-specific PCR primers are similar to those used for in silico PCR.
The user chooses Group-specific PCR on the PCR Primer Design tab. After specifying inputs and PCR primer design options, the user can execute the PCR primer design task. The programme takes either multiple separate DNA sequences in FASTA or at alignment formats. Once the primer set design is complete, the result will appear in Result text editor, as the PCR primer design result.
The result text editor PCR primer design result displays the individual group-specific PCR primer design data, including the primer list and compatible primer pairs for all the sequences and their internal tasks where suitable primers are found. In the case where an alignment has been input, the result text editor displays only one the group-specific PCR primer design set, including degenerate primers, in the primer list as well compatible primer pairs for all the sequences.

Unique PCR

The strategy for a unique PCR primer design is opposite to the group-specific PCR primers (probes) design. This case program search unique regions within a DNA sequence and automatically designing primers with minimal user intervention and maximum flexibility.