Introduction

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.

Publications

  1. Primaclade--a flexible tool to find conserved PCR primers across multiple species.
    Cite this
    Gadberry MD, Malcomber ST, Doust AN, Kellogg EA, 2005-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Michael D Gadberry
    Developer

  2. Simon T Malcomber
    Developer

  3. Andrew N Doust
    Developer

  4. Elizabeth A Kellogg
    Investigator

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Summary
AccessionBT006543
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByElizabeth A Kellogg