Introduction | Description | Tests | Summary | References | FAQ | Program Interface
Primaclade is a web-based application that accepts a multiple species nucleotide alignment file as input and identifies a set of PCR 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 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.
| Figure 1. Opening Screen. |
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| Figure 2. A. Primaclade output screen showing primers identified in the 5' region of the KN1 gene. Upper block consists of aligned sequences, middle block the consensus. Conserved bases are shown in colored text, non-conserved in black. Bottom four lines list primer sequences, followed by the number of the start position, Tm, %GC content, and length. Orange primers have one or two degenerate bases, red have three or more. B. Primaclade output screen showing primers identified in the 3' region of the KN1 gene. Display similar to 2A, but green primers are non-degenerate. Reverse complements are provided to the right (off the screen in this display). |
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Primaclade Interface (opens in new window)