Extensive research over the past two decades has shown there is a remarkably consistent conservation of gene order within large segments of linkage groups in agriculturally important grasses such as rice, maize, sorghum, barley, oats, wheat, and rye. Grass genomes are substantially colinear at both large and short scales with each other, opening the possibility of using syntenic relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum.
As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the grass genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other grass species. This is achieved by building automated and curated relationships between cereals for both sequence and biology. The automated and curated relationships are queried and displayed using controlled vocabularies and web-based displays. The controlled vocabularies (Ontologies), currently being used include Gene ontology, Plant ontology, Trait ontology, Environment ontology and Gramene Taxonomy ontology. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database.