ArticleBiotechnology research international2013
Family-specific degenerate primer design: a tool to design consensus degenerated oligonucleotides.
Article in Biotechnology research international, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Optimized Design of Degenerate Primers for PCR Based on DNA or Protein Sequence Comparisons.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- Article
- In silico design and validation of a highly degenerate primer pair: a systematic approach.Journal, genetic engineering & biotechnology · 2020Article
- Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals.PLoS neglected tropical diseases · 2018Article
- MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR.Nucleic acids research · 2015Article
- Generation of Optimized Consensus Sequences for Hepatitis C virus (HCV) Envelope 2 Glycoprotein (E2) by a Modified Algorithm: Implication for a Pan-genomic HCV Vaccine.Avicenna journal of medical biotechnologyArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 × 10(4) nucleotides), Baculovirus (0.9 × 10(5) to 1.8 × 10(5) bp), Lactobacillus sp. (1 × 10(6) to 2 × 10(6) bp), and Pseudomonas sp. (4 × 10(6) to 7 × 10(6) 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.
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