SNP-Seek database of SNPs derived from 3000 rice genomes

被引：259

作者：

Alexandrov, Nickolai ^{[1
]}

Tai, Shuaishuai ^{[2
]}

Wang, Wensheng ^{[3
]}

Mansueto, Locedie ^{[1
]}

Palis, Kevin ^{[1
]}

Fuentes, Roven Rommel ^{[1
]}

Ulat, Victor Jun ^{[1
]}

Chebotarov, Dmytro ^{[1
]}

Zhang, Gengyun ^{[2
]}

Li, Zhikang ^{[3
]}

Mauleon, Ramil ^{[1
]}

Hamilton, Ruaraidh Sackville ^{[1
]}

McNally, Kenneth L. ^{[1
]}

机构：

[1] IRRI, TT Chang Genet Resources Ctr, Los Banos 4031, Laguna, Philippines

[2] BGI, Shenzhen 518083, Peoples R China

[3] Chinese Acad Agr Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Inst Crop Sci, Beijing 100081, Peoples R China

来源：

NUCLEIC ACIDS RESEARCH | 2015年 / 43卷 / D1期

关键词：

FRAMEWORK;

D O I：

10.1093/nar/gku1039

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

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.

引用

页码：D1023 / D1027

页数：5

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