In this project, we use unified standard SNP-calling pipeline for SNP-calling.
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.
From another point of view, you can restrict the variation itself, for instance, minor allele frequency, position and the variant type of the variation.
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.
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 These results are scattered in the literature and different kinds of websites based on outdated and puzzling genome versions, which is absolutely unhelpful to basic research and applied research in rice.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 (1)SNP information, (2)population diversity in the total samples and different groups, (3)genotype information of each accessions, (4)annotation information, (4)related gene summary and their (6)associated traits.
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.
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.
The process could take a while, the work page will redirect to results if it is done.
results can be
download and the phylogenetic tree can be visualized with tree view tools.
You can save the job ID to check it at any time within a week.
We implement three kinds of frequently used population genetics parameters' calculators. They can calculate the ? (Watterson estimator), Tajima's D and ? (nucleotide diversity). You can select the specific genomic intervals and set up the window size and step size in an appropriate range. The result will be displayed as publishing-styled tables, which is easy to be download.
For example, here is the illustration of how use the Population Genetic Analysis Toolbox.
We construct the haplotype by taking the information out of our variation database based on the region of each gene and its 3000 base pairs? flank sequence upstream and downstream beforehand. You can extract gene?s specific haplotype to display and down load the result in tsv format.