Designing multiple degenerate primers via consecutive pairwise alignments.
BACKGROUND
Different algorithms have been proposed to solve various versions of degenerate primer design problem. For one of the most general cases, multiple degenerate primer design problem, very few algorithms exist, none of them satisfying the criterion of designing low number of primers that cover high number of sequences. Besides, the present algorithms require high computation capacity and running time.


RESULTS
PAMPS, the method presented in this work, usually results in a 30% reduction in the number of degenerate primers required to cover all sequences, compared to the previous algorithms. In addition, PAMPS runs up to 3500 times faster.


CONCLUSIONS
Due to small running time, using PAMPS allows designing degenerate primers for huge numbers of sequences. In addition, it results in fewer primers which reduces the synthesis costs and improves the amplification sensitivity.
Najafabadi
Hamed Shateri
HS
Nanobiotechnology Research Center, Avesina Research Institute, Shahid Beheshti University, Evin Ave., Tehran, Iran. hamed.shaterinajafabadi@mail.mcgill.ca
Torabi
Noorossadat
N
Chamankhah
Mahmood
M
D000465:Algorithms; D001483:Base Sequence; D017931:DNA Primers / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D017931:DNA Primers