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diff --git a/academic/amplicon/README b/academic/amplicon/README index 395b56f031..de8c35014b 100644 --- a/academic/amplicon/README +++ b/academic/amplicon/README @@ -1,3 +1,15 @@ +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 @@ -5,6 +17,13 @@ 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. |