Family-Specific Degenerate Primer Design : A Tool to Design Consensus Degenerated Oligonucleotides
Joint Authors
Iserte, Javier Alonso
Ghiringhelli, Pablo Daniel
Lozano, Mario Enrique
Goñi, Sandra Elizabeth
Borio, Cristina Silvia
Stephan, Betina Ines
Source
Biotechnology Research International
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-02-21
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Information Technology and Computer Science
Abstract EN
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 (10×104 nucleotides), Baculovirus (0.9×105 to 1.8×105 bp), Lactobacillus sp.
(1×106 to 2×106 bp), and Pseudomonas sp.
(4×106 to 7×106 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.
American Psychological Association (APA)
Iserte, Javier Alonso& Stephan, Betina Ines& Goñi, Sandra Elizabeth& Borio, Cristina Silvia& Ghiringhelli, Pablo Daniel& Lozano, Mario Enrique. 2013. Family-Specific Degenerate Primer Design : A Tool to Design Consensus Degenerated Oligonucleotides. Biotechnology Research International،Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-467779
Modern Language Association (MLA)
Iserte, Javier Alonso…[et al.]. Family-Specific Degenerate Primer Design : A Tool to Design Consensus Degenerated Oligonucleotides. Biotechnology Research International No. 2013 (2013), pp.1-9.
https://search.emarefa.net/detail/BIM-467779
American Medical Association (AMA)
Iserte, Javier Alonso& Stephan, Betina Ines& Goñi, Sandra Elizabeth& Borio, Cristina Silvia& Ghiringhelli, Pablo Daniel& Lozano, Mario Enrique. Family-Specific Degenerate Primer Design : A Tool to Design Consensus Degenerated Oligonucleotides. Biotechnology Research International. 2013. Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-467779
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-467779