SNP和等位基因信息被组织成一个SNP-Seek系统(http://www.oryzasnp.org/iric-portal/),该系统由Oracle数据库组成,该数据库具有SNP基因型接近600亿的行总数(20 M个SNP x 3 K水稻行)和Web界面,方便查询。该数据库允许快速检索给定基因组区域中所有变种的SNP等位基因,从预定的变种中查找不同的等位基因,并查询有...
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93...
1.首先在SNP-Seek(https://snp-seek.irri.org/)中,进入Genotypes, 2.在Gen locus,输入基因ID(注意是LOC_类型的),并且可以在START和End中自行选择所要分析基因位置,然后在Show phenotype中选择是要分析的表型,完成后点击SEARCH. 3.分析好后,点击CSV,将结果下载下来。(切记在CSV文件中不要做任何处理,改文件格式...
Intact RNA-seq datasets were deposited in the NCBI Gene Expression Omnibus (GEO) under accession numberGSE168650. The Rice SNP-Seek Database is accessible athttps://snp-seek.irri.org/; the EnsemblPlants database is accessible athttp://plants.ensembl.org/index.html.Source dataare provided with...
Rice SNP-seek database update: new SNPs, indels, and queries Authors: Locedie Mansueto, Roven Fuentes, Frances Nikki Borja … Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals Authors: Wei-Wei Chen, Wensheng Wang, Meng-Meng Peng … Differentiall...
SNP-Seek: the Largest Database of Rice Natural Variations.Nickolai Alexandrov
The non-synonymous mutation SNPs in the exon region of all genes in the interval were extracted from 3KRGP’s RiceSNP-SeekDatabase website (https://snp-seek.irri.org/). These SNPs were used to perform haplotype analysis of all genes in the interval using DnaSP software. For genes with ...
Mansueto L, Fuentes RR, Borja FN, Detras J, Abriol-Santos JM, Chebotarov D, Sanciangco M, Palis K, Copetti D, Poliakov A, Dubchak I, Solovyev V, Wing RA, Hamilton RS, Mauleon R, McNally KL, Alexandrov N (2017) Rice SNP-Seek database update: new SNPs, indels, and queries. ...
et al. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res. 45, D1075–D1081 (2017). Article CAS Google Scholar Wang, W. S. et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 43–49 (2018). Article CAS Google ...
The RNA-sequencing data have been deposited in NCBI’s Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo/) under accession number GSE161265. Data from the 3K Rice Genomes Project can be downloaded from Rice SNP-Seek Database (https://snp-seek.irri.org/). Soil nitrogen content data are ...