The system will start at different modules when the user queries FASTSNP in different ways. When the user queries FASTSNP by gene, the query module will be used to check a cross-reference table and convert the query term to Ensembl Gene Name (16). The cross-reference table combines a set of widely used gene nomenclatures, including HUGO Gene Symbol, HUGO Gene Aliases (17), NCBI Reference Sequence (RefSeq) (18) and SwissProt Entry Name and users can query FASTSNP with these gene nomenclatures. With the converted gene name, we can extract a set of SNPs on the queried gene from the EnsemblMart database.
