SNP-Seek database of SNPs derived from 3000 rice genomes

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...

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Detalles Bibliográficos
Autores principales: Alexandrov, Nickolai, Tai, Shuaishuai, Wang, Wensheng, Mansueto, Locedie, Palis, Kevin, Fuentes, Roven Rommel, Ulat, Victor Jun, Chebotarov, Dmytro, Zhang, Gengyun, Li, Zhikang, Mauleon, Ramil, Hamilton, Ruaraidh Sackville, McNally, Kenneth L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Database Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383887/
https://www.ncbi.nlm.nih.gov/pubmed/25429973
http://dx.doi.org/10.1093/nar/gku1039
Descripción
Sumario: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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