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The number of copies of each sample transcript was then determined with the aid of the LightCycler software.
Each sample transcript was assayed in triplicate and copy numbers were indicated for each transcript.
The sample transcript assemblies were then merged with reference annotations (WBcel235) using Cuffmerge to generate a single, overall transcript assembly.
To account for expression bias due to transcript length, each sample transcript expression was normalized by using Cufflinks algorithm with an FDR of 0.05.
In cufflinks, per sequenced sample, transcript identity and abundance were statistically estimated and computed as expected number of fragments per kilobase of exon per million fragments mapped (FPKM) (Trapnell et al. 2010, 2012).
Prediction of secondary structure in a sample transcript using a standard nucleic acid secondary structure prediction algorithm (Mfold) demonstrates that while longer-range interactions are reduced at high temperatures, stable local structures persist in the transcript even at high salt concentration and high temperature.
Similar(53)
(A and B ) Sample transcripts exhibiting translation in alternate frames.
In BC-1, another KSHV-positive/EBV-positive PEL cell line, transcripts from 34 annotated and 4 unannotated/novel KSHV genes were detected over the reference sample; transcripts from 22 annotated and 1 novel EBV genes were detected.
In JSC-1, a KSHV-positive/EBV-positive PEL cell line, transcripts from 67 annotated and 6 unannotated/novel KSHV genes were detected over the reference sample; transcripts from 41 annotated and 2 novel EBV genes were detected.
The frequency of miRNAs in the two libraries was normalised to one million by the total number of miRNAs in each sample (transcripts per million (TPM) normalised expression = initial miRNA count*1,000,000/total count of clean reads).
Formally, define a p.d.f f for a randomly sampled transcript to have normalized-expression ν.
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