Improved algorithms for multiplex pcr primer set selection with amplification length constraints

K. M. Konwar, I. I. Mǎndoiu, A. C. Russell, A. A. Shvartsman

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 reaction (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 exponentially 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.

Original languageEnglish (US)
Title of host publicationProceedings of the 3rd Asia-Pacific Bioinformatics Conference, APBC 2005
PublisherImperial College Press
Pages41-50
Number of pages10
ISBN (Print)1860944779, 9781860944772
DOIs
StatePublished - 2005
Externally publishedYes
Event3rd Asia-Pacific Bioinformatics Conference, APBC 2005 - Singapore, Singapore
Duration: Jan 17 2005Jan 21 2005

Publication series

NameSeries on Advances in Bioinformatics and Computational Biology
Volume1
ISSN (Print)1751-6404

Conference

Conference3rd Asia-Pacific Bioinformatics Conference, APBC 2005
Country/TerritorySingapore
CitySingapore
Period1/17/051/21/05

ASJC Scopus subject areas

  • Bioengineering
  • Information Systems

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