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Brief introduction about the search engine

We designed a powerful search engine for our variation database. Here we collected a great deal of information among the findings of rice genomic research into our database. Our search conditions are ingenious, which can help you determine appropriate constraints in order to locate the results you want precisely.

  1. You can select samples directly as you like; or select the attributes attached in the samples, for examples, subpopulation information of the samples.

  2. From another point of view, you can restrict the variation itself, for instance, minor allele frequency, position and the variant type of the variation.

  3. Better and better, from our database, you can retrieve the information of the Gene annotation, Gene ontology, KEGG pathways, and so forth. Since variation makes a difference mainly in the coding region, of which the biological functions are vital, these information could really help a lot in your studies.

  4. Last but not least, we devised the search interface for the information from QTL (quantitative trait loci), trait ontology and GWAS (Genome Wide Association Study) results. These results are scattered in the literature and different kinds of websites based on outdated and puzzling genome versions, which is absolutely unhelpful to basic research and applied research in rice.

    You can find the SNP information (1), population diversity (2) in the total samples and different groups, genotype information (3) of each accessions, annotation information (4), related gene summary (5) and their associated traits (6).

Brief introduction about the three practical online tools

  1. RiceClustw

    On the one hand, you can query your own sequence to reveal the genetic relationship to our 5K samples by nucleotide BLAST. This BLAST programs search in rice variation databases with a nucleotide sequence query.

    On the other hand, you can select any sample in our database as you request and any genomic region to perform a multiple sequence alignment.

    Furthermore, in either case, you can reconstruct phylogenetic trees based on the pairwise distance matrix from selected sequences using Neighboring-joining algorithm. All of these functions are easily visualized and all the results can be exported to your local disk freely.

  2. Population Genetic Analysis Toolbox

    You can extract specific haplotype to display and analyze selected samples from our database. We constructed the haplotype by taking information out of our variation database based on the region of each gene and its 3000 base pairs? flank sequence upstream and downstream beforehand.

    1. Haplotype display:You can easily find that how many haplotypes exist in the rice 5K population and their specific bases.
    2. Haplotype network:We also implement the pegas (R, Population and Evolutionary Genetics Analysis System) to perform haplotype network analysis.
    3. Haplotype phylogeny: You can also reconstruct the haplotype phylogenetic tree using samples you need in a specific region.

    For example, here is the illustration of how use the Population Genetic Analysis Toolbox.