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The genome was digested with the MspI enzyme, a methylation-insensitive restriction enzyme.
In the process of selection of an optimal enzyme, the reference genome was digested in silico with each of ten methylation-sensitive enzymes.
The reference genome was digested in silico and the predicted coverage compared to that of the aligned consensus sequences is shown in Table 2.
The genome was digested singly BamHI, tandem dimers were ligated with T4 DNA ligase, and the dimeric genomes inserted into the BamHI site of the pBluescript SK (pSK) vector (Stratagene).
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This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme.
Whole DNA genomes were digested with Hinf1 and Sau3AI, labeled with a fluorescent tag of Cy3 and then hybridized.
To create a phage as a recombinant between two parental phages, the two genomes were digested with a restriction enzyme with a unique site in the genome.
The BOP method is applied to a set of finished (completely sequenced and closed) genomes as follows: The genomes are digested in silico with one of several restriction enzymes to produce an ordered restriction map.
The two genomes were digested with RsrII (which cuts near the 3′ end of gene 9), complementary fragments were ligated, and the mix was transfected into cells with pSW5 (T3 gene 10) to obtain isolates that were then tested on a host with pRK11 (K11 gene 10).
To release the RabX1 or RabX2 locus from the genome, DNA was digested with PstI and SacII.
To determine the copy number of PSY gene in the genome of C. zofingiensis, genomic DNA was digested with two different restriction enzymes (either HincII or HindIII) and subjected to Southern blot analysis at different conditions of stringency.
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