Given a set of SNPs, FASTSNP will dispatch the dbSNP agent to query dbSNP (19) for their genomic context sequences, their mRNA reference sequences (RefSeq), and their relative locations in gene sequences (e.g. 5′ upstream, 5′-UTR, non-synonymous, intronic and so on). Next, FASTSNP will prepare a set of sequences for each SNP as the input of the function analysis module. Each sequence is a 41 bp fragment trimmed from the genome sequence with the SNP allele exactly in the middle.
