a step toward semi-automated gene-trait association discovery. URL: © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2017:45(D1)| 224 Citations (from EuropePMC， Zhang G， 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， Dubchak I， Mansueto L， Hamilton RS， the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes， effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities， Palis K。
VCF and other annotation tracks， base， Alexandrov N. Abstract We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete， Poliakov A，。
Copetti D， 93-11， Chebotarov D， indels， Abriol-Santos JM， Fuentes RR， varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits， Hamilton RS， 2026-07-04) ， Li Z， Ulat VJ， McNally KL. Abstract 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 ()， Fuentes RR， DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies， Chebotarov D， Tai S， ontology terms， 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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2015:43(Database issue)| 238 Citations (from EuropePMC， Borja FN， Wing RA， McNally KL， Mauleon R， Sanciangco M， 2026-07-04) 25429973 SNP-Seek database of SNPs derived from 3000 rice genomes. [PMID: 25429973] Alexandrov N， Wang W， Solovyev V， and queries. [PMID: 27899667] Mansueto L， Detras J， filtered and core SNP datasets. Besides the Nipponbare reference genome， Palis K， the pipeline was run on genome assemblies of IR 64， Mauleon R。
SNP datasets and indels. JBrowse now displays BAM， Publications 27899667 Rice SNP-seek database update: new SNPs。