文献类型： 外文期刊
第一作者： Alexandrov, Nickolai
作者： Alexandrov, Nickolai;Mansueto, Locedie;Palis, Kevin;Fuentes, Roven Rommel;Ulat, Victor Jun;Chebotarov, Dmytro;Mauleon, Ramil;Hamilton, Ruaraidh Sackville;McNally, Kenneth L.;Tai, Shuaishuai;Zhang, Gengyun;Wang, Wensheng;Li, Zhikang
作者机构：
期刊名称：NUCLEIC ACIDS RESEARCH （ 影响因子：16.971； 五年影响因子：15.542 ）
ISSN： 0305-1048
年卷期： 2015 年 43 卷 D1 期
页码：
收录情况： SCI
摘要： We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes project with the Nipponbare genome. The SNPs and allele information are organized into a SNP-Seek system (http://www.oryzasnp.org/iric-portal/), which consists of Oracle database having a total number of rows with SNP genotypes close to 60 billion (20 M SNPs x 3 K rice lines) and web interface for convenient querying. The database allows quick retrieving of SNP alleles for all varieties in a given genome region, finding different alleles from predefined varieties and querying basic passport and morphological phenotypic information about sequenced rice lines. SNPs can be visualized together with the gene structures in JBrowse genome browser. Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.
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