The function analysis module consists of three agent pipelines corresponding to decision paths in the decision tree shown in Figure 1. The first pipeline is for non-coding SNPs. The input sequence pair will be sent to TFSearch (20) to obtain the predicted transcription factor-binding sites. The second pipeline handles non-synonymous SNPs. In this pipeline, an agent will query PolyPhen (21) to obtain its prediction on whether the SNP will alter an amino acid in a protein and result in structural changes (damaged or benign) in the protein. The third agent pipeline obtains information to predict if the alternative splicing caused by a synonymous SNP may abolish a protein domain. FASTSNP will first invoke the agents for ESEfinder (22), RESCUE-ESE (23) and FAS-ESS (24) to predict if the SNP is located in an exonic splicing enhancer or silencer motif. It then invokes another agent to query Ensembl Protein Report (16) and obtain all known alternative spliced-form mRNAs for the gene where the SNP is located. With the spliced form mRNAs, the agent for SwissProt (15) will be able to extract the
