mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-16 19:50:19 +01:00
29 lines
1.6 KiB
Text
29 lines
1.6 KiB
Text
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.
|