primers4clades --Phylogenetic PCR Primer Design
What you can do:
Design PCR primers for DNA from different species.
Highlights:
- Primers4clades is a 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.
- It 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.
Keywords:
- PCR
- polymerase chain reaction
- PCR primer
- PCR oligo
- oligonucleotide
- phylogeny
Literature & Tutorials:
This record last updated: 09-25-2009