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Data for these marker sets have been submitted to the CottonGen SNP database (http://www.cottongen.org).org
Two recent studies, examining larger cohorts and using denser marker sets, have been more successful.
However, implementing this method becomes more challenging with increasing ploidy, and not all marker sets have consistent enough amplification to confidently employ this method.
Finally, haplotype block and haplotype-tagging SNP analyses have been suggested to only be reliable when markers are dense, otherwise marker sets have considerable loss of information[ 50].
However, only a few predictive marker sets have yet been successfully validated for routine use in the clinic (van de Vijver et al, 2002; Paik et al, 2004).
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We analyzed the banding patterns in the most widely adopted sugarcane bioethanol strains and in several indigenous yeast contaminants, and found that our marker set had very good discriminatory power.
The pervasive usage of this marker set has led to the development of functional assays based on multiplex PCR and multi-color capillary gel electrophoresis.
Furthermore, a high-resolution association map created using a high-density marker set has the potential to unravel stress-associated genetic variability in a genome [ 10].
The noted weaknesses in the use of solely performance indicators for marker discovery, without considering the stability of the proposed marker set, has been raised in the literature [ 34] and is in congruence with the findings of this study.
Several linkage maps of various sizes, marker sources and completeness are available, however, no integrated map and marker set has explored consistency of linkage analysis among unrelated mapping populations.
Furthermore, we have used a case only study design, which for a given sample size and marker set, has been suggested by others to be more powerful than a case control study design (reviewed in Montana et.al [ 42]).
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