We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover,...
k-mers方法的top特征关联强于SNP的top特征,甚至比在拟南芥或玉米中看到的更为强烈。 SNP- and k-mer-based GWAS in tomato. 结论:研究结果证明了k-mers结合GWAS的能力,可以检测出与表型变异相关的、更广泛的遗传变异。 本文提出了一种基于k-mers的GWAS方法,并将其与传统的基于SNP的方法直接比较了来自三个不同...
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS. workflow bioinformatics gwas snakemake pipeline genomics ngs conda bioinformatics-pipeline structural-variation gwas-pipeline bioinformatics-tool gwas-tools kmers sciworkflows association-mapping Updated Jul 13, 2023 Python armin...
Δmoccs2scores, suggesting that cd gwas-snps include snps that both potentially attenuate and intensify the binding of fos and spi1. consistently, we found that the alt- k -mer of rs56167332 (ggaagt, Δmoccs2score < 0) corresponded to the motif of spi1, and the ref- k -mer of...
Kassemble is a Python package with the objective to assemble denovo contigs and scaffolds using a reference-free, k-mer based approach. kassemble incorporates the SPAdes software tool and/or SOAPdenovo2 tool as a Python wrapper to create contigs of unique k-mers extracted from reads in a fa...
应用于细菌基因组的全基因组关联研究(GWAS)方法在发现遗传标记或详细评估标记效应方面显示了良好的结果。最近,基于k-mer组成的无比对方法证明了其探索副基因组的能力。然而,它们会导致冗余的描述和结果,有时很难解释。这里我们介绍DBGWAS,一个扩展的基于k-mer的GWAS方法,产生与不同表型相关的可解释的遗传变异。我们...
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to desig...
Next, fluorescence studies revealed thatMGis weakly fluorescent. WhenMG(10 μM) (λex = 265 nm) was titrated withh-TELO(0–6 μM) in 100 mM KCl, 10 mM HEPES at pH 7.4, a dose-dependent increase in fluorescence intensity (λem = 355 nm) ofMGwas observed (Fig...
Diseases such as Alzhei- mer's disease and inflammatory bowel disease (IBD) were found to have overlapping GWAS-identified loci with our PM2.5-associated H3K27ac markers. Discussion Accumulating evidence has demonstrated that PM is able to induce systemic inflammatory responses by altering the ...
文献:Interpreting k-mer–based signatures for antibiotic resistance prediction 中文:解释基于k-mer信号的抗生素耐药性预测 杂志:gigascience 单位:法国某单位 时间:2020.10.17 摘要: 背景 近年来出现了几种基于k- merk的方法,旨在根据细菌的全基因组序列预测其表型特征。虽然在预测性能方面常常令人信服,但基本模型通...