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Given the difficulties with multiple gene comparisons, a cohort of this size would be insufficient to arrive at meaningful conclusions if the effect sizes are small.
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We extended our pairwise analysis to multiple gene order comparisons.
We selected 17 high-coverage vertebrate genome assemblies from the EnsEMBL database (release 50) to run multiple gene order comparisons.
Since none of the aforementioned methods worked for our multiple gene order comparison in vertebrates, we compared CYNTENATOR CSMs to a set of multiple vertebrate species syntenic blocks defined by Larkin et al. [25].
Although we could not validate our microarray data using different RNA methods such as the quantitative reverse transcription polymerase chain reaction (RT-PCR), our conclusion is supported by consistent results from multiple gene set comparison analyses.
Typing markers were found by multiple genome and gene comparisons, from which 23 canonical single nucleotide polymorphisms (canSNPs) and 11 canonical insertion-deletion mutations (canINDELs) were selected to provide phylogenetic guidelines for classification from genus to isolate level.
Although gene expression data can also be inconsistent between experiments, and some reactions are associated with multiple genes, this comparison further supports the qualitative results presented in the previous section.
The ideal model system would provide multiple gene rearrangements for comparison (to identify common themes), but in a lineage that is not rearranging so frequently that hidden and convergent rearrangements obscure the interpretation of evolutionary events.
We improved on the efficiency of our approach by recasting it into a profile-profile alignment setting, which is an extension of the Waterman-Eggert algorithm [21] to the comparison of multiple gene orders.
Consequently, the comparison of multiple gene trees is the only way to get a central tendency which could be interpreted as the species tree [ 61- 63].
The well-established differential screening technology, that allows for the simultaneous comparison of multiple gene expression levels between two samples differing in tissue type and pathological state, has been the more extensively applied.
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