Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides
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 mult...
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| Veröffentlicht in: | Biotechnology Research International 2013-01, Vol.2013 (2013), p.39-47 |
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| container_title | Biotechnology Research International |
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| creator | Iserte, Javier Alonso Stephan, Betina Ines Goñi, Sandra Elizabeth Borio, Cristina Silvia Ghiringhelli, Pablo Daniel Lozano, Mario Enrique |
| description | 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. |
| doi_str_mv | 10.1155/2013/383646 |
| format | Article |
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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.</description><identifier>ISSN: 2090-3138</identifier><identifier>ISSN: 2090-3146</identifier><identifier>EISSN: 2090-3146</identifier><identifier>DOI: 10.1155/2013/383646</identifier><identifier>PMID: 23533783</identifier><language>eng</language><publisher>Cairo, Egypt: Hindawi Limiteds</publisher><subject>Analysis ; Arenavirus ; Collections ; Computer programs ; Deoxyribonucleic acid ; Design ; DNA ; Genomes ; Microbiology ; Primers (Molecular genetics) ; Proteins</subject><ispartof>Biotechnology Research International, 2013-01, Vol.2013 (2013), p.39-47</ispartof><rights>Copyright © 2013 Javier Alonso Iserte et al.</rights><rights>COPYRIGHT 2013 John Wiley & Sons, Inc.</rights><rights>Copyright © 2013 Javier Alonso Iserte et al. 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.</rights><rights>Copyright © 2013 Javier Alonso Iserte et al. 2013</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a5786-1beac22cd99c3e568e7705c81fc46f43b5ebcacabc1cca51d4c83496e08556973</citedby><cites>FETCH-LOGICAL-a5786-1beac22cd99c3e568e7705c81fc46f43b5ebcacabc1cca51d4c83496e08556973</cites><orcidid>0000-0002-8469-4833 ; 0000-0002-2003-0106 ; 0000-0001-9828-3616 ; 0000-0003-0056-1177</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600133/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600133/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23533783$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Laible, Goetz</contributor><creatorcontrib>Iserte, Javier Alonso</creatorcontrib><creatorcontrib>Stephan, Betina Ines</creatorcontrib><creatorcontrib>Goñi, Sandra Elizabeth</creatorcontrib><creatorcontrib>Borio, Cristina Silvia</creatorcontrib><creatorcontrib>Ghiringhelli, Pablo Daniel</creatorcontrib><creatorcontrib>Lozano, Mario Enrique</creatorcontrib><title>Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides</title><title>Biotechnology Research International</title><addtitle>Biotechnol Res Int</addtitle><description>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. 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| ispartof | Biotechnology Research International, 2013-01, Vol.2013 (2013), p.39-47 |
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| source | PubMed Central Open Access; Wiley-Blackwell Open Access Titles; EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Analysis Arenavirus Collections Computer programs Deoxyribonucleic acid Design DNA Genomes Microbiology Primers (Molecular genetics) Proteins |
| title | Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides |
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