Designing multiple degenerate primers via consecutive pairwise alignments

Hamed Shateri Najafabadi,Noorossadat Torabi,Mahmood Chamankhah

doi:10.1186/1471-2105-9-55

Abstract

BackgroundDifferent 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.ResultsPAMPS, 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.ConclusionDue 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.

Highlights

Different algorithms have been proposed to solve various versions of degenerate primer design problem
We introduce a new algorithm for solving Multiple Degenerate Primer Design (MDPD) problems which consecutively uses an ad hoc pairwise alignment for multiple primer selection – called PAMPS
Each set contained 20–100 sequences with similar length, but the lengths of sequences varied among different sets; sequences were of lengths 15–50 nucleotides

Summary

Introduction

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. In order to use PCR, one must know the exact sequences which lie on either side of the DNA region of interest. These sequences are used to design two synthetic DNA oligonucleotides, or primers, one complementary to each strand of the DNA double-helix and lying on opposite sides of the target region. Degenerate primers are useful for amplifying several related genomic or cDNA sequences, and have been exploited in various applica-

Methods

Results

Conclusion