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High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa) can be effectively utilized for whole genome genotyping to conduct mutant mapping and analysis of quantitative traits such as gene expression levels.
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Table 1 shows the results of both the genome and transcript mappings.
We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets.
For both steps, it is imperative to consider conflicts between the reference genome and transcript libraries.
Comparison between genome and transcript sequences using common numerous specimens may resolve this uncertainty.
These optimizations greatly improve SFP detection performances in both whole-genome and transcript hybridizations.
Between these two sets of genes, 25 were identified in common to both genome- and transcript-aligned reads.
(A complete overview can be found in the online bioinformatic databases of genome and transcripts, protein structure, and brain expression).
EGFP cells were isolated by FACSorting, DNA and RNA were extracted and analysed by PCR and RT-PCR for the presence of virus genome and transcripts.
Causes of low sensitivity in SFP detection would be different for whole-genome and transcript hybridizations.
Finally, a comparison of benefits and limitations of SFP detection by whole-genome and transcript hybridization approaches was made.
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