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During assembly, 19 reads caused slippage error messages from CAP3 and were therefore removed.
Experimentally, we determined the in vitro DNA polymerase-mediated strand slippage error rates as a function of repeat number.
Slippage error creates a loop in one of the strands that gives rise to an insertion or a deletion in the subsequent replications, depending on the strand specificity (replicating or template strand) of loop formation.
So, one can postulate that pol III makes a slippage error in the run of three T residues and stops at or before the cross-link, when a TLS polymerase is recruited.
We measured polymerase frameshift errors at the monitors to evaluate the background polymerase strand slippage error frequency within a representative coding sequence, analogous to the background slippage rates measured using repeat size polymorphism for monitors in the computational analysis above.
Our analysis suggests that, to become a sustainable microsatellite, a short tandem repeat needs to meet a minimal size requirement that allows it to acquire slippage rates higher than the overall genome slippage error rate and, according to our experimental results, to overcome the directionality bias that favors deletion errors.
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It is possible to implement basic models to approximate and correct offset and slippage errors on-line leading to significant improvement of performances.
To examine the mechanisms underlying these biases, we investigated the roles of DNA polymerase slippage errors and MMR.
We used an in vitro mutagenesis assay to evaluate the contribution of strand slippage errors to mutability.
Microsatellites are highly unstable, that is, the number of repeat units tends to change due to slippage errors during DNA replications.
We emphasize that strand slippage errors occur at both microsatellites and shorter repeats; however, the dynamic mutational behavior is acquired only as the tandem repeat array lengthens.
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