PRIMACLADE

Welcome to The Santos Lab implementation of Primaclade (Gadberry et al. 2005, BioInformatics 21:1263-1264), a web-based application developed by The Kellogg Lab (University of Missouri-St. Louis) that accepts a multiple species nucleotide alignment file as input and identifies a set of PCR (Polymerase Chain Reaction) primers that will bind across the alignment. The Primaclade program iteratively runs the Primer3 application for each alignment sequence and collates the results. The user may adjust a number of parameters to improve and refine the results. These options include: 1) the maximum number of degenerate base pairs allowed, 2) the number of gapped lines in the alignment to ignore, 3) a region of the alignment to exclude for primer discovery, 4) the primer melting temperature and 5) the approximate GC content of the primer. Primaclade creates an HTML results page (and text file) that recaps the original alignment, provides a consensus sequence and lists primers for each alignment area. In addition, the generated primers are color-coded to reflect the level of degeneracy in the primer. Primaclade is being run at the AU Dept. of Biological Sciences on an Apple G5 14-processor computer cluster affectionately known as GUMP (Genomics Using Multiple Processors). For optimal performance and results, your input file should have UNIX line breaks and limit the alignment to no more than 8 sequences of <29% divergence (see cited paper for details). WARNING: old result files are automatically purged from GUMP on a weekly basis, so download your data in a timely fashion.