Efficient primer design algorithms

Abstract

The reference point method was found to be tractable for trading-off between deviations from ideal values of all the criteria. Some criteria computations are based on dynamic programs with value iteration whose run time can be bounded by a low-degree polynomial. For designing standard PCR primers, the scheme offers in a relative gain in computing speed of up to 50: 1 over ad-hoc computational methods. Single PCR primer pairs have been used as model systems in order to simplify the quantization of the computational acceleration factors. The program has been structured so as to facilitate the analysis of large numbers of primer pairs with minor modifications. The scheme significantly increases primer design throughput which in turn facilitates the use of oligonucleotides in a wide range of applications including: multiplex PCR and other nucleic acid-based amplification systems, as well as in zip code targeting, oligonucleotide microarrays and nucleic acid-based nanoengineering.

ProGene 1.0-An In Silico Tool for Protein-Gene Analysis

“…Another important application of ProGene1.0 is to provide the detailed information of the nucleotide sequences via Nucleic acids Composition. It predicts total number of nucleotide sequences, total composition of Adenine (A) and Thiamine (T) combination as well as Guanine (G) and Cytosine (C) combination [16][17] , to know the stability of DNA structure [18] and the GC content percentage especially for the optimized primer design [19] . As a result ProGene 1.0 enables more flexibility and expandability compared with other online tools.…”

Confronting two-pair primer design for enzyme-free SNP genotyping based on a genetic algorithm

“…To date, many primer design approaches have been proposed, such as dynamic programming [29], parthenogenetic algorithm MG-PGA [30], greedy algorithm [31], heuristic algorithm [32], genetic algorithm [21,33], memetic algorithm [28] and any others. However, most of these methods do not provide the SNP genotyping function.…”

A Customized Simulated Annealing Suitable for Primer Design in Polymerase Chain Reaction Processes

“…It is important to mention, however, that all the attempts to define a proper value for T m are only an approximation of the real melting temperature since, as commented in (Kämpke et al, 2001), "A proper computation of the primer melting temperature does not appear to exist". a comparative study of different melting temperature calculation methods as well as the influence of the different NN interaction values available for the T m calculations is presented in (Panjkovich & Melo, 2005).…”

“…The sec_struc_cost function takes into consideration only the annealing situation with the highest cost per group (highest_cost(G i )). The cost of any annealing situation is given as the sum of the numbers of A-T matches (costs 2 each) and C-G matches (costs 4 each), as suggested in (Kämpke et al, 2001). The pseudocode of the implemented SA algorithm is given in Fig.…”