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It is critical to design compatible multiple primer sequences and conditions when several PCR reactions may interfere reciprocally in a tube.
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Using multiple primer pairs along the sequence might alleviate this problem to some extent, but if these primers were designed from a single sequence, they will on average be biased towards sequences that are similar to the template sequence.
We amplified and sequenced a broad ensemble of partially-rearranged molecules at each time interval using multiple sets of PCR primers (primer sequences are listed in Methods S1; positions are shown in Figure 3 and Figure S1).
The (multiple) different combinations of alternative primer sequences due to the inclusion of degenerate primer bases were not checked for adherence to PRIMER3 primer design criteria prior to ordering the primer sets due to the complexity of performing this task.
A fully comprehensive analysis of non-TIR NBS-LRR sequences in M. acuminata will require multiple primer sets, together with more exhaustive sequencing of amplicons.
The combination of 16S rRNA gene amplification using multiple primer sets and the subsequent sequencing of the PCR products by Roche 454 pyrosequencing should therefore be a powerful method to assess the diversity of the microbiota in the GI tract of common carp.
Indeed, frequently yields greater than 100% are observed, suggesting multiple primer initiations per parent DNA sequence.
Redundancy reduction using in silico PCR and BLAST analysis against the TrGT database prevented retention of multiple primer pairs for a single sequence or legitimate members of the same contig.
It should be noted that the use of multiple primer sets biases the number of sequences belonging to the identified taxa.
These degenerate bases were placed at the sites where a base mismatch occurred between the zebra finch and chicken sequence in an attempt to make the primer sequences amplify in multiple species.
Accordingly, we designed multiple primer sets for MSP and bisulfite sequencing that spanned the entire ACVR2 promoter region, including part of exon 1, to determine methylation density across all CpG dinucleotides with methylation specific primers (see Table S1).
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