The PhyloPrimer website is no longer active. The source code behind PhyloPrimer can be found
in the PhyloPrimer GitHub page. Please email gilda.varliero@wsl.ch for any query.
WHAT'S PHYLOPRIMER
PhyloPrimer was born from a collaboration between the University of Bristol and ENOVEO (https://enoveo.com), a company
involved in bioremediation and microbial monitoring projects that looks into a wide variety of
environmental samples with the aim of identifying specific genes and microorganisms. The idea was to
create a user- friendly platform to i) easily retrieve DNA sequences similar to a gene of interest, ii)
design oligos (e.g. primer and probes) suitable for different PCR applications, iii) check the oligos
for the presence of secondary structures and iv) study each oligo with in silico tests for determining
which organisms they can potentially target. The strength of PhyloPrimer is the possibility of
retrieving the DNA sequences, used for the oligo design, through a dynamic tree. The tool was designed
with the study of microbial communities in mind, so we do not encourage the use of PhyloPrimer for the
study of eukaryotic organisms: the dynamic tree is built only with microorganism sequences and the tool
does not take in consideration the presence of intron regions. Also, PhyloPrimer uses a consensus
approach and will introduce degenerate primers only if necessary and if specified by the user, but we do
not suggest the use of it if the aim is specifically to design degenerate primers. PhyloPrimer database is
a modified version of the GenBank database (release 241) and it was last updated in April 2021.
GET STARTED
PhyloPrimer can be used both for designing new oligos or checking your own oligos. The tool will work
with three different modalities in relation your starting data:
1. The first modality involves the dynamic tree visualization. If you
want to amplify a gene or region of interest but first you want to explore similar DNA sequences before
proceeding to the primer design, please click on the following button.
2. If you want to design oligos with PhyloPrimer and you already have
all the DNA sequences you want PhyloPrimer to use for the oligo design, please click on the following
button.
3. If you already have your oligos and you want to check them through
PhyloPrimer, please click on the following button.
MORE ABOUT THE TOOL
Please visit the GitHub page to have more information about the tool.
Refer to DOI:10.7717/peerj.11120 to cite the tool and see applications of PhyloPrimer.
