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While this framework map is reasonably comprehensive, it will undoubtedly evolve with the addition of more markers, allowing the establishment of linkage on unrepresented chromosomes, and refining interval orders for those existing linkage groups.
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Diagnostic SNP information alone might be sufficient to assign the M. m. domesticus origin in most regions, however for regions of M. m. musculus or M. m. castaneus origin diagnostic VINOs enrich the information and help to refine interval boundaries and avoid incorrect assignment.
As the ability to refine intervals increases, one possible outcome is that the number of candidate loci could increase with some Idd regions being subdivided further.
Future studies will focus on refining this interval by the ascertainment of additional deletion cases.
To refine this interval we tested ten additional deficiencies with three of them interacting and seven failing to interact (Table 2).
The inclusion of additional micro-satellite markers in the region defined by rs13477916 and rs3091114 further refined the interval to suggest that the disease locus lay in a 5.3-cM region between rs13477959 and rs3091114 (Supplementary Fig. S6, Table S2).
CMA further identified the additional material of unknown origin and delineated breakpoints on all derivative chromosomes, thereby often having the added advantage of refining genomic intervals involved in the imbalance (N = 26) such as in case V4-31, case V5-41 and case V5-35 (Table S1 and S2).
In this study, we refined the interval containing the QTL responsible for ear size on SSC5 from an 11 cM interval to an 8.7 cM region.
Homozygosity analysis refined the interval to a 3.4-Mb region containing the SLC4A2 gene, encoding an anion exchanger protein necessary for proper osteoclast function.
In an attempt to further refine the interval identified above, we mined all genotyped accessions for which protein data were available, regardless of maturity group or environment.
BAIT accurately refines the interval between reads in which the template switch occurs, allowing regions with a high propensity to undergo SCE to be identified (for example, fragile sites [ 26] or sites of recurrent DNA damage).
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