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On sequencing the recovered PCR products, the expected sequences were obtained.
Data processing and analyses were performed using custom Perl scripts and the statistical programming environment R. Fastq sequence reads with missing bases or barcodes not matching any of the expected sequences were excluded (if applicable).
Computational Analysis of Small RNA High-Throughput Sequencing Data Data processing and analyses were performed using custom Perl scripts and the statistical programming environment R. Fastq sequence reads with missing bases or barcodes not matching any of the expected sequences were excluded (if applicable).
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These results are summarized in Figure 5 and Additional files 3 and 4. The expected sequences are reported and the identified peptides are highlighted or underlined.
In both cases, plasmids possessing the expected sequence were purified using the QIAprep spin miniprep kit (Qiagen #27106) from 3 5 mL LB cultures grown for 16 20 h at 37°C.
After PCR amplification using sunflower genomic DNA as template, products with the expected sequence were obtained for 10/19 loci.
While deviations from the expected sequence are observed they are restricted to point mutations and small indels which can be attributed to the fidelity of the polymerases used for the PCR amplification.
Clones from which the expected sequence was confirmed were transferred to the pCB302-3 vectors.
For this reason, these results are summarized in Figure 7, in which the expected sequence is reported and the identified peptides are underlined.
Only the positive PCR results with the expected sequence profiles were scored and analyzed further.
As expected, these sequences were mainly associated to photosynthesis.
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