SNP-Seek: the Largest Database of Rice Natural Variations.N. Alexandrov
1.首先在SNP-Seek(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,改文件格式无法保存...
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...
Rice Stress-Resistant SNP database (http://bioinformatics.fafu.edu.cn/RSRS) mainly focuses on SNPs specific to biotic and abiotic stress-resistant ability in rice, and presents them in a unified web resource platform. The Rice Stress-Resistant SNP (RSRS) database contains over 9.5 million stres...
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. ...
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...
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...
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 ...
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 ...
The 3 K phenotype data were obtained from RFGB (https://www.rmbreeding.cn/Phenotype). The dataset used for population evolutionary analysis was down- loaded from the rice SNP Seek database (https://snp- seek.irri.org/_download.zul). ...