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The analysis of the results with Coffalyser.net showed a duplication (value of 1.68) for the exon 9 of CHEK2 in patient III-4 (data not shown).
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Caenorhabditis elegans-specific duplications were added to Lophotrochozoa-specific duplications to get a total duplications value for "non-arthropod protostomes".
Conclusive evidence for a general trend of positive selection was not found for the set of genes, since nearly all ω values were much less than one, though there were a few higher post-duplication values that suggested some duplicates may have been influenced by directional selection.
We defined genes with increased copy number as those with a log2 aCGH ratio greater than 0.7 (because relative intensity values are often slightly compressed from the expected duplication log2 value of 1.0); genes with a log2 aCGH ratio < −1.0 were identified as potentially deleted.
However, our results are altogether encouraging and show that our methods yield biologically significant predictions of orthologs when the duplication bonus value is properly chosen.
LIG1 duplication (Ks value 0.39) was quite newer but locus AT1G49250 showed an intron gain in comparison to locus AT1G08130.
Duplication span values for duplicate pairs in this dataset ranged from 128 – 10,646 bp with a median value of 1,670 bp.
First, to avoid expansion process duplication, the values of the objective function and constraint functions for parameter V i,G are stored in the variables.
Our results suggest that after gene duplication, pI values in the PGI-1 clade gradually decreased, whereas those in the PGI-2 clade increased.
We conducted a search for HGT and duplication cost values which lead to minimum average genome flux (the difference between the ancestor and descendant genome sizes over every lineage of the species tree).
Excluding unmapped contigs, pericentromeric regions represent 3.4% of genomic sequence, but show an enrichment of 2.4-fold for duplications (p-value < 0.001) and contain 8.1% of all duplicated bases.
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