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This was applied in some particular cases when the LOD curve of the single QTL genome scan method displayed two distinct LOD peaks for a given linkage group.
To address this problem and to enhance the utility more generally of the association-based studies carried out in inbred lines of mice, we proposed a combination linkage and association approach that incorporated molecular profiling data to identify genes responsible for a given linkage (Cervino et al. 2005).
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Distorted markers were retained for mapping, if their presence did not alter the surrounding marker order in a given linkage group (LG).
Methods that are optimized for computational speed that also correct for multiple tests appropriately given linkage disequilibrium and non-independent multilocus models under consideration are needed to effectively search the genome for gene-gene interactions.
Factors contributing to this genetic complexity include QTL previously detected as single QTL fractionating into multiple QTL for a given trait, tight linkages among QTL for multiple traits, the presence of previously unmapped horticultural trait QTL, and QTL with opposite directionality of allelic effects in different environments.
The permutation procedure flips transmitted/untransmitted status constantly for all SNPs for a given family, thereby preserving the linkage disequilibrium and linkage information between markers and siblings.
In this way, linkage groups were created between markers that were linked with a two-point LOD score > 5, had a minimum of 0.4 times the average number of meioses, shared linkages with no more than six other groups and had a minimum linkage ratio (i.e. the proportion of two point linkages for a given marker to other markers in the same linkage group) of 0.5.
However, there was no repeatable pattern of linkage disequilibria across populations; linkage disequilibrium for a given pair of loci was almost always detected in a single population only.
For instance, in order to find the possible in-directed linkage for a given gene-compound pair, we can look up the four extended associations in Chem2Bio2RDF: gene-disease-compound, gene-compound-compound, gene-pathway-compound, and gene-gene-compound, and then compute the association scores for the outputs from Chem2Bio2RDF.
The initial ability to match on a patient-level using the unique NHS number allowed us to restrict the number of possible linkages for a given patient.
Finally, the "Cross" term is a bonus score added for cross-species hits for a given gene except for genes from human linkage regions.
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