Oligonucleotide (primer) design for polymerase chain reaction (PCR)
experiments is an important stage in successfully obtaining desired PCR
products (amplicons). PCR primer design may be assisted by software that
helps the user assess features of the oligonucleotides that determine
how they may interact with each other and with target and non-target DNA
sequences in a solution. The design of PCR primers where multiple target
sequences may be present in a solution is a difficult problem. This
situation has not been extensively investigated and is difficult to
address with software solutions, especially given a surprising lack of
knowledge relating to Tm calculation of mismatched oligonucleotide and
target sequences.

Amplicon is a tool for designing PCR primers where groups of related 
DNA sequences can be assessed in aligned form. Other useful features 
that are not common in other PCR primer design software are handling 
of gapped sequences and degenerate sites in aligned DNA. Amplicon can 
import aligned DNA sequences produced by Clustal, or aligned 
sequences in MEGA or Fasta format.

Amplicon can import aligned DNA sequences produced by ClustalW or
ClustalX (Thompson et al., 1997); or aligned sequences in MEGA (Kumar et
al., 1997) or Fasta format. Primer analyses can be saved to text files
for editing in any text editor or word processor. Alignments that have
been altered in Amplicon can be saved in Fasta, MEGA, .aln, PAUP
(Swofford, 2003) or Phylip (Felsenstein, 1993) formats.

For details and citation:
Jarman SN (2004) Amplicon: software for designing PCR primers on 
aligned DNA sequences. Bioinformatics 20: 1644-1645.