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We first analyzed the relative position of mutations along the length of chromosomes irrespective of sequence features, normalizing mutation positions to the position along the chromosome from 0 to 100%.
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The RefSeq sequence was used to calculate position frequency matrices, detection of new mutation positions, and to estimate distances from RefSeq to the FLIC and RefSeq to new mutants we planned on introducing into the FLIC.
Alanine scanning mutagenesis and homology modeling have suggested a spiral pattern on the S4 domain of residues mutations to which perturb activation, with inactivation-perturbing mutation positions mapped to a distinct face of the S4 helix [38,45].
Stratification by mutation position relative to amino acid 1042 (nucleotide 4213) divided the BRCA2 carrier sample into two subgroups of 42 and 177 individuals.
The variations observed between the two types of fusion curves obtained depend on whether the base at the mutation positions was complementary to the probes [ 14].
Our results show that alterations to mutation position are restricted to a subset of genes in modified genomes.
Because these interaction motifs are grouped into pairs of complementary motifs, correlated mutation positions were compared both to individual motifs and to pairs of complementary motifs.
They are at nucleotide position 39 (A to T) in the 5′ UTR, position 1,531 (C to T) in the structural protein E region resulting in a serine to phenylalanine mutation, position 3,511 (A to T) in the non-structural protein region resulting in a histidine to leucine mutation, and position 3,468 (A to C) in the non-structural protein region resulting in a methionine to leucine mutation.
Mutation positions were assigned according to the following human mRNA reference sequences: NM_006244 (PPP2R5B), NM_001161725 (PPP2R5C) and NM_006245 (PPP2R5D).
First, we utilized the mutation positions from COSMIC data to map the gene regions using the UCSC Genome Browser based on the GRCh37 genome annotation [ 28].
In contrast, the L363E mutation positions an anionic carboxylate adjacent to the phosphonyl-enzyme intermediate to activate a water molecule for nucleophilic attack.
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