ArticleNucleic acids research2009
primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 27 citations in OpenAlex.
- Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity.Applied and environmental microbiology · 2024Article
- Recombinant production and characterization of a novel esterase from a hypersaline lake, Acıgöl, by metagenomic approach.Extremophiles : life under extreme conditions · 2019Article
- Self-Conjugation of the EnteropathogenicBioMed research international · 2017Article
- Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in theFrontiers in microbiology · 2017Article
- Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species.Frontiers in plant science · 2017Article
- Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition.Genome biology and evolution · 2016Article
- PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection.Scientific reports · 2016Article
- Article
- PrimerView: high-throughput primer design and visualization.Source code for biology and medicine · 2015Article
- A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil.Nucleic acids research · 2012Article
- In silico analyses of primers used to detect the pathogenicity genes of Vibrio cholerae.Microbes and environments · 2012Article
- PhyDesign: an online application for profiling phylogenetic informativeness.BMC evolutionary biology · 2011Article
- maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences.Bioinformatics (Oxford, England) · 2011Article
- Deep sequencing of a dimethylsulfoniopropionate-degrading gene (dmdA) by using PCR primer pairs designed on the basis of marine metagenomic data.Applied and environmental microbiology · 2010Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms, belonging to user-specified phylogenetic clades or taxa. The server takes a set of non-aligned protein coding genes, with or without introns, aligns them and computes a neighbor-joining tree, which is displayed on screen for easy selection of species or sequence clusters to design lineage-specific PCR primers. Primers4clades implements an extended CODEHOP primer design strategy based on both DNA and protein multiple sequence alignments. It evaluates several thermodynamic properties of the oligonucleotide pairs, and computes the phylogenetic information content of the predicted amplicon sets from Shimodaira-Hasegawa-like branch support values of maximum likelihood phylogenies. A non-redundant set of primer formulations is returned, ranked according to their thermodynamic properties. An amplicon distribution map provides a convenient overview of the coverage of the target locus. Altogether these features greatly help the user in making an informed choice between alternative primer pair formulations. Primers4clades is available at two mirror sites: http://maya.ccg.unam.mx/primers4clades/and http://floresta.eead.csic.es/primers4clades/. Three demo data sets and a comprehensive documentation/tutorial page are provided for easy testing of the server's capabilities and interface.
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