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For these two pairs of transcripts, the biotinylated probes used to detect transcription on both strands were designed approximately at the same coordinates, indicating that the observed transcripts are complimentary to each other for most of their lengths.
Using images of pairs of transcripts that are often co-transcribed, we discuss how selection of cell type, design of FISH probes, image acquisition, and image processing affect the precision that can be achieved.
In the mouse genome, Kiyosawa et al. [33] identified 899 pairs of transcripts, in which one transcript lies in an intron(s) of another transcript and has an opposite orientation.
Positive correlated expression patterns between pairs of transcripts are often domain-specific for putative structured ncRNAs.
Pearson (PC) and Spearman correlation (SC) for pairs of transcripts and respective proteins were calculated to depict relationships.
Pairs of transcripts with an E-value of 10-50 or less were defined to be equal.
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In the Blast analysis two types of alignments were exploited: "exact alignment", i.e. 100% sequence identity over 25 base pairs of transcript and probe sequence, and "near-exact alignment" with at most one mismatch (identity of 24 base pairs).
Among the 3,585 pairs of transcript compared, the average Ka/Ks ratio is 0.225.
Considering pairs of orthologous genes, each encoding a set of alternative transcripts, we can detect pairs of transcript variants employing identical exon-intron structures, i.e. orthologous splicing variants, with other variants being species-specific or lacking characterized orthologous counterparts.
The average of the CV for all the pairs of transcript tags was 26.1% before drought (DW0) and 20.2% after drought (DW2) after filtering out tags with < 2 RPKM.> -wrap-foot> Results were partitioned between over and under-expressed and the magnitude of difference (fold) in the sensitive and tolerant pools relative to the control.
In principle, a one-to-one mapping of reconstructed transcripts to expressed transcripts could be achieved by finding pairs of equal transcripts between the expressed transcripts and the assembled transcripts.
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