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Briefly, we first filtered the 454 small RNA sequence libraries by removing sequences that match previously characterized miRNAs, Ae. aegypti transposable elements (TEfam: http://tefam.biochem.vt.edu), and other known mosquito non-coding RNAs.
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The proteins identified were similar to those from previous studies and the quantitative profiles largely matched those previously characterized.
Cluster, AAC01781 which was identified as a singleton matched a previously characterized LEA protein from desiccated A. avenae [ 9].
This dynamic proteomic profiling identified 721 actively synthesized proteins with significant temporal changes in expression throughout the light-dark cycles, of which 425 proteins matched with previously characterized cycling transcripts.
Three of these cps loci matched those previously characterized in the ST11 reference genome HS11286 (genotype wzi-74/ cpserotype, serotype K74) and in ST258/512 K. pneumoniae (genotypes wzi-29/cps207-2 and wzi-154/ cpsBO-4; unknown serotypes) (Chen et al. 2014; D'Andrea et al. 2014; Deleo et al. 2014).
Of the 721 labeled proteins identified in this study, 425 proteins (58.9%) matched with the previously characterized cycling transcripts.
Specifically, we identified 721 proteins actively synthesized over the time course, of which 425 proteins matched with the previously characterized cycling transcripts [ 12].
Most SNPs matched the expected positions (previously characterized), although in a few cases additional SNPs were also segregating.
This does not match the consensus sequence of any previously characterized Alu subfamily.
In addition to lacking the CpG mutation at position 64, loci 8, 116, and 327 of the Yb7 elements also shared three additional unique modifications (G to A at position 207, C to T at position 243, and G to A at position 268) which do not appear to match the consensus sequence of any previously characterized Alu subfamily.
We have not found any matches between these RNA sequences and previously characterized or predicted non-coding RNAs whose sequences are available in RNA databases.
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