Name
Title | ||
|---|---|---|
Improved algorithms for multiplex PCR primer set selection with amplification length constraints |
Abstract | ||
|---|---|---|
Numerous high-throughput genomics assays require the amplification of a large number of genomic loci of interest. Amplification is cost-effectively achieved using several short single-stranded DNA sequences called primers and polymerase enzyme in a reaction called multiplex polymerase chain re- action (MP-PCR). Amplification of each locus requires that two of the primers bind to the forward and reverse DNA strands flanking the locus. Since the efficiency of PCR amplification falls off ex- ponentially as the length of the amplification product increases, an important practical requirement is that the distance between the binding sites of the two primers should not exceed a certain threshold. In this paper we study MP-PCR primer set selection with amplification length constraints from both theoretical and practical perspectives. Our contributions include an improved analysis of a simple yet effective greedy algorithm for the problem, and a comprehensive experimental study comparing our greedy algorithm with other published heuristics on both synthetic and genomic database test cases. |
Year | Venue | DocType |
|---|---|---|
2005 | APBC | Conference |
Citations | PageRank | References |
1 | 0.51 | 11 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Kishori M. Konwar | 1 | 107 | 17.49 |
| Ion I. Mandoiu | 2 | 372 | 47.28 |
| Alexander Russell | 3 | 529 | 56.75 |
| Alexander A. Shvartsman | 4 | 766 | 58.27 |