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On the basis of their amino acid sequences, we designed and synthesized 3′ RACE and 5′ RACE primer.
Based on intron sequences, we designed specific primers capable of identifying C. orthopsilosis and C. metapsilosis species, and we reidentified species among the initial isolates.
Based on the analysis of 61 full-length COI sequences, we designed four pairs of mini-barcode primers: Tu-A, Tu-B, Tu-C and Tu-D.
On the basis of these sequences, we designed 6 forward primers at the variable region and 5 reverse primers at the joining region.
According to the nucleotide sequences, we designed and synthesized five pairs of sequence characterized amplified regions (SCAR) primers to identify the specific fragments in these gynogenetic clones of silver crucian carp.
After selecting and extracting target gene sequences, we designed probes as diagrammed in Figure 1.
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Based on the canine Y-chromosome sex-determining region (Sry) sequence, we designed primer specific for the detection of male DNA and optimised PCR conditions and cycle numbers.
Thus, in order to standardize the number of amplified DNA copies before sequencing, we designed a PCR re-amplification protocol.
Based on the unique sequence variations within each MHC sequence, we designed primers to specifically amplify genomic sequences spanning exon 1, intron 1, exon 2, intron 2, and exon 3, using LR PCR and exon-localized primers (Table S3).
To avoid assembly errors from homopolymer runs (characteristics of the pyrosequencing technology) and to acquire a high-quality complete cp genome sequence, we designed 151 pairs of primers covering the preliminary cp genome assembly.
After sequencing, we designed microsatellite primers using the software Primer3 (Rozen and Skaletsky, 1999).
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