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29 lines
1.6 KiB
Text
29 lines
1.6 KiB
Text
Oligonucleotide (primer) design for polymerase chain reaction (PCR)
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experiments is an important stage in successfully obtaining desired PCR
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products (amplicons). PCR primer design may be assisted by software that
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helps the user assess features of the oligonucleotides that determine
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how they may interact with each other and with target and non-target DNA
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sequences in a solution. The design of PCR primers where multiple target
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sequences may be present in a solution is a difficult problem. This
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situation has not been extensively investigated and is difficult to
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address with software solutions, especially given a surprising lack of
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knowledge relating to Tm calculation of mismatched oligonucleotide and
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target sequences.
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Amplicon is a tool for designing PCR primers where groups of related
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DNA sequences can be assessed in aligned form. Other useful features
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that are not common in other PCR primer design software are handling
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of gapped sequences and degenerate sites in aligned DNA. Amplicon can
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import aligned DNA sequences produced by Clustal, or aligned
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sequences in MEGA or Fasta format.
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Amplicon can import aligned DNA sequences produced by ClustalW or
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ClustalX (Thompson et al., 1997); or aligned sequences in MEGA (Kumar et
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al., 1997) or Fasta format. Primer analyses can be saved to text files
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for editing in any text editor or word processor. Alignments that have
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been altered in Amplicon can be saved in Fasta, MEGA, .aln, PAUP
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(Swofford, 2003) or Phylip (Felsenstein, 1993) formats.
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For details and citation:
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Jarman SN (2004) Amplicon: software for designing PCR primers on
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aligned DNA sequences. Bioinformatics 20: 1644-1645.
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