Bioinformatics Vol. 17 no. 3 2001
Pages 214-225
© 2001 Oxford University Press
Original Paper |
Efficient primer design algorithms
1 Forschungsinstitut
für anwendungsorientierte
Wissensverarbeitung FAW, Helmholtzstr. 16, 89081 Ulm, Germany
2 jSoft GmbH, Bahnhofstr. 7, 73447
Oberkochen, Germany
3 INTERACTIVA Bioteknik AB & BT
Biomedical Technology, IDEON Research Park, Ole
Römersväg
12, S 223 70 Lund, Sweden
Received on March 8, 2000
; revised on September 14, 2000
; accepted on October 19, 2000
Motivation: Primer design involves various parameters such as string-based alignment scores, melting temperature, primer length and GC content. This entails a design approach from multicriteria decision making. Values of some of the criteria are easy to compute while others require intense calculations.
Results: The reference point method was found to be tractable for
trading-off between deviations from ideal values of all the
criteria. Some criteria computations are based on dynamic programs
with value iteration whose run time can be bounded by a low-degree
polynomial. For designing standard PCR primers, the scheme offers in
a relative gain in computing speed of up to 
over ad-hoc
computational methods. Single PCR primer pairs have been used as
model systems in order to simplify the quantization of the
computational acceleration factors. The program has been structured
so as to facilitate the analysis of large numbers of primer pairs
with minor modifications. The scheme significantly increases primer
design throughput which in turn facilitates the use of
oligonucleotides in a wide range of applications including:
multiplex PCR and other nucleic acid-based amplification systems, as
well as in zip code targeting, oligonucleotide microarrays and
nucleic acid-based nanoengineering.
Availability: A public version of the software DOPRIMER is accessible under http://doprimer.interactiva.de
Contact: kaempke{at}faw.uni-ulm.de
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