Simulate_PCR statistics

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Simulate_PCR specifications

Information


Unique identifier OMICS_05372
Name Simulate_PCR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Simulate_PCR

Simulate_PCR in publications

 (5)
PMCID: 4602216
PMID: 26459131
DOI: 10.1038/srep14629

[…] branching process model of pcr (‘model 1’) where the efficiency of the pcr (between 0 and 1) refers to the probability that a molecule will replicate successfully in a cycle. using this model, we simulate pcr and sampling, and show that the resulting barcode family size distributions do not diverge significantly from the expected poisson distribution regardless of the efficiency used (). […]

PMCID: 4361551
PMID: 25774512
DOI: 10.1371/journal.pone.0122004

[…] (16s rrna) on a bacterial chromosome and beta-actin gene (actb) on a mammalian chromosome were designed as internal controls. amplifx 1.7.0 (http://crn2m.univ-mrs.fr/pub/amplifx-dist) was used to simulate pcr reaction using the newly designed primers., 1accession no. indicates genbank accession number of reference sequence., multiplex pcr was carried out using a takara multiplex pcr assay […]

PMCID: 4137498
PMID: 25157264
DOI: 10.1155/2014/101894

[…] mhv, the primers from parts 0, 2, and 4 were combined in one reaction and the primers from parts 1 and 3 were combined in another, so that short products would not be produced., we used the script simulate_pcr.pl (https://sourceforge.net/projects/simulatepcr/ []) to predict all pcr amplicons from the multiplex degenerate primers compared to the target sequences and to the ncbi nt database. […]

PMCID: 3980782
PMID: 24778651
DOI: 10.1155/2014/720585

[…] (ttmv) (20 genomes, samples 11 and 14), echovirus 9 (7 genomes, validation for sample 5), and rotavirus a (7077 sequences, all segments, for sample 5). predicted targets were identified using simulate_pcr.pl (submitted, https://sourceforge.net/projects/simulatepcr) based on comparison to the llnl large (48 gb) internal database of all available finished and assembled microbial genomes […]

PMCID: 3852801
PMID: 23339526
DOI: 10.1186/1756-0500-6-25

[…] using ten different empirical distributions corresponding to adjacent windows covering 200 flow cycles. a refinement of this simulator was presented in a subsequent paper [], in which balzer et al. simulate pcr amplification errors at a rate estimated by analysing ‘sub- peaks’ of flowgram values over the integer values adjacent to the correct value. mcelroy et al. [] propose a simulator capable […]


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Simulate_PCR institution(s)
Computations/Global Security, Lawrence Livermore National Laboratory (LLNL), Livermore, CA, USA

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