Sentence examples for implemented primer from inspiring English sources
Extensive optimisation steps were required to achieve proper functioning of implemented primer pairs in one PCR reaction and finally simultaneous detection of all desired groups of bacteria.
Relationships between phylogenetic distances of bacterial communities and soil properties were assessed by Mantel tests as implemented in PRIMER v6 (Clarke and Gorley [2006]).
Some missing environmental data were extrapolated by applying the expectation maximum likelihood algorithm implemented in Primer 7 (1000 iterations, minimum value change: 10−6).
Mantel tests as implemented in PRIMER v6 were also assessed to analyze the relationships between phylogenetic distances of bacterial communities and soil properties.
Correlation between eubacterial and archaeal ARISA resemblance matrices and environmental variables (log-transformed) were tested via the BEST tool implemented in Primer 7 (BIOENV method using Spearman rank correlation).
Primer-BLAST also supports placing primers based on exon/intron locations and excluding single nucleotide polymorphism (SNP) sites in primers.We describe a robust and fully implemented general purpose primer design tool that designs target-specific PCR primers.
Furthermore, a Primer3 web-server [ 40] was implemented to enable PCR primer design on the assembled sequences.
To enable in silico analysis of these probes for possible hybridization with other transcripts, we constructed a Perl script to identify matches of >10 nt in the transcribed portion of any annotated genome (in GenBank or Ensembl format), estimating the Tm of each target and off-target match by the method of Allawi et al.[ 14] as implemented in the BioPerl Primer module.
Primer3 (Rozen and Skaletsky, 2000) is implemented in MSATCOMMANDER for primer design according to the following criteria: amplification products within the size range of 100 500 bp, optimal melting temperature (range 57 62°C), optimal GC content of 50%, possession of at least 1-bp GC clamp, low levels of self- or pair-complementary, and maximum end stability (ΔG) of 8.0 (Faircloth, 2008).
Primer design for the additional PCR amplification and sequencing primers was implemented using the Primer3 software (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi).
