title: MAD-DPD: designing highly degenerate primers with maximum amplification specificity.
abstract: This work introduces minimum accumulative degeneracy, a variant of the degenerate primer design problem, which is particularly useful when a large number of sequences are to be covered by a set of restricted number of primers. A primer set, which is designed on a minimum accumulative degeneracy basis, especially helps to reduce nonspecific PCR amplification of undesired DNA fragments, as fewer primer species are present in PCR. A Boltzmann machine is designed to solve the minimum accumulative degeneracy degenerate primer design problem, called the MAD-DPD Boltzmann machine. This algorithm shows great flexibility, as it can be determined either to solve the problem with strict fidelity to covering all input sequences or to exclude some input sequences if it results in less degenerate primers. This Boltzmann machine is successfully implemented in designing a new set of primers for amplification of antibody variable fragments from mouse spleen cells, which theoretically covers more diverse antibody sequences than currently available primers. The MAD-DPD Boltzmann machine is available online at bioinf.cs.ipm.ir/download/MAD_DPD08172007.zip.
authors.affiliation: McGill University, Montreal, QC, Canada.
authors.forename: Hamed Shateri
authors.initials: HS
authors.lastname: Najafabadi
authors.forename: Amir
authors.initials: A
authors.lastname: Saberi
authors.forename: Noorossadat
authors.initials: N
authors.lastname: Torabi
authors.forename: Mahmood
authors.initials: M
authors.lastname: Chamankhah
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers / Q000737:chemistry* / Q000235:genetics*; D018076:DNA, Complementary / Q000096:biosynthesis / Q000235:genetics; D007128:Immunoglobulin Fragments / Q000235:genetics; D051379:Mice; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D016133:Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D013816:Thermodynamics
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D007128:Immunoglobulin Fragments