title: Primaclade--a flexible tool to find conserved PCR primers across multiple species.
abstract: Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of polymerase chain reaction (PCR) primers that will bind across the alignment. Primaclade iteratively runs the Primer3 application for each alignment sequence and collates the results. Primaclade creates an HTML results page that recaps the original alignment, provides a consensus sequence and lists primers for each alignment area, with primers color-coded to reflect the level of degeneracy in the primer.
authors.affiliation: Department of Biology, University of Missouri-St. Louis, One University Boulevard, St. Louis, MO 63121, USA.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Gadberry
authors.forename: Simon T
authors.initials: ST
authors.lastname: Malcomber
authors.forename: Andrew N
authors.initials: AN
authors.lastname: Doust
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Kellogg
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D017124:Conserved Sequence; D017931:DNA Primers / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013045:Species Specificity
chemical_list: D017931:DNA Primers