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Biotechnology Research International
Volume 2013 (2013), Article ID 383646, 9 pages
Research Article

Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides

1LIGBCM-Área Virosis Emergentes y Zoonóticas, Universidad Nacional de Quilmes, B1876BXD Buenos Aires, Argentina
2LIGBCM-Área Virosis de Insectos, Universidad Nacional de Quilmes, B1876BXD Buenos Aires, Argentina

Received 15 October 2012; Accepted 11 January 2013

Academic Editor: Goetz Laible

Copyright © 2013 Javier Alonso Iserte et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four different genome collections were used, covering a wide range of genomic lengths: Arenavirus ( nucleotides), Baculovirus ( to  bp), Lactobacillus sp. ( to  bp), and Pseudomonas sp. ( to  bp). In each case, FAS-DPD designed primers were tested computationally to measure specificity. Designed primers for Arenavirus and Baculovirus were tested experimentally. The method presented here is useful for designing degenerate primers on collections of related protein sequences, allowing detection of new family members.