G e n e S i e v e

If you have a fasta file of candidate genes, please enter a description of a plant trait you are interested in, and please upload the fasta file of the candidate genes for that plant trait. After pressing submit, GeneSieve will return a search result custom to your inputted plant trait and candidate genes.

If you are just interested in a demo, please select a plant trait. After pressing submit, GeneSieve will return a pre-computed search result.

The resolution of most genetic experiments is limited and cannot accurately determine the single gene that is causing a trait. Usually, the resolution ranges from 20 to 100 genes. GeneSieve’s goal is to prioritize these genes based on previously determined associations between a trait and a genomic sequence from four model crop species. After doing a genetic experiment (in any species), the researcher can submit a set of genes as well as a natural language description of the trait, such as would be found in the literature.

The GeneSieve database is essentially an association graph with two terminal nodes: the entered gene and the trait description. Each gene in the entered list spawns a set of paths through the association graph. The current graph has four types of weighted links – 1) protein similarity, 2) coexpression, 3) genetic association, and 4) trait similarity. All links are weighted from 0 to 1 based on biological criteria. For each gene the user has submitted, GeneSieve finds all cycles through the graph that connect that gene with the submitted trait through the existing database. The higher the path score and the more independent paths involved, then the more likely that candidate is.