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This mapping allows us to accurately determine the effect of genomic variants on transcripts, and to determine the genomic context of variants found in transcripts.
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We have developed MU2A, a publicly available web service for variant annotation that reconciles differences between the genome and transcriptome, enabling the rapid and accurate determination of the effects of genomic variants on protein products, and the mapping of variants detected in transcripts to genomic coordinates.
Also, effects of genomic variants, especially CNV, on tissue-specific expression patterns, as well as alternative splicing and epigenetic modifications need to be considered.
This unexpected effect is largely due to mutations located in non-canonical regulatory elements and highlights the difficulty in correctly predicting the consequence of genomic variants on pre-mRNA splicing (4– 8).
These variables may have technology- and coverage-specific effects on the detection of genomic variants.
Other examples are the 1000 genomes project data, the Database of Genomic Variants [34], and more local databases like LuCamp containing 700.000 SNPS from 2000 Danish individuals [35].
The Database of Genomic Variants currently listed more than 15,000 CNV loci in the human genome (The Database of Genomic Variants 2013).
The new CNVs information is available from DGV (Database of Genomic Variants).
There are similarly small and non-exonic entries in the Database of Genomic Variants (Figure 1).
Then, oligodendroglioma structural variants were compared against variants in the Database of Genomic Variants (DGV).
Our copy number variation data were compared to the Database of Genomic Variants [ 19] to exclude genomic variants.
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