Open AccessSNP-Seek database of SNPs derived from 3000 rice genomes
Author(s) -
Nickolai Alexandrov,
Shuaishuai Tai,
Wensheng Wang,
Locedie Mansueto,
Kevin Palis,
Roven Rommel Fuentes,
Victor Jun Ulat,
Dmytro Chebotarov,
Gengyun Zhang,
Zhikang Li,
Ramil Mauleon,
Ruaraidh Sackville Hamilton,
Millicent D. Alexandrov Sanciangco
Publication year - 2014
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gku1039
Subject(s) - biology , genome , genetics , single nucleotide polymorphism , genome browser , snp , molecular inversion probe , tag snp , computational biology , genomics , gene , genotype
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 × 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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