This application allows a thermodynamic analysis of the sequencing primers the program uses by default the parameters (annealing temperature and component concentrations) related to the Sanger sequencing reaction. The user can modify them using 'Advance setting' In addition to the temperature, it also returns the possible secondary structures (hairpin-loop, self-dimeri) that the primers form at the annealing temperature (chosen by the user). The primer sequences are also analyzed for the base content, for the presence of similar base stratches and for the stability of the 3' The program will show as output, a penalty to evaluate the 'goodness' of the sequence and possibly the percentage of primers forming structures. By clicking on the appropriate links, you can view the details of the penalty and details of any facilities. The percentages of primers forming structures are calculated with thermodynamic hybridization parameters at the annealing temperature. For any secondary structures at 3', a lower temperature is adopted. The structures are determined using a special program that thermodynamically analyzes the hybridization of short sequences.
the program uses by default the parameters (annealing temperature and component concentrations) related to the Sanger sequencing reaction. The user can modify them using 'Advance setting'
In addition to the temperature, it also returns the possible secondary structures (hairpin-loop, self-dimeri) that the primers form at the annealing temperature (chosen by the user).
The primer sequences are also analyzed for the base content, for the presence of similar base stratches and for the stability of the 3'
The program will show as output, a penalty to evaluate the 'goodness' of the sequence and possibly the percentage of primers forming structures.
By clicking on the appropriate links, you can view the details of the penalty and details of any facilities.
The percentages of primers forming structures are calculated with thermodynamic hybridization parameters at the annealing temperature. For any secondary structures at 3', a lower temperature is adopted.
The structures are determined using a special program that thermodynamically analyzes the hybridization of short sequences.