An Example of user-specific database construction. To construct a user-specific database, the user needs to provide a FASTA file containing sequences of interest and a flat information file documenting the SAPs/PTMs and disease information that the user wishes to consider. In this example, Id_Seq1 and Id_Seq2 represent sequence identifiers. In the information file, the format is as follows. First column indicates residue position; second column specifies whether the modification is a SAP or PTM; third column records the original residue in the sequence at position specified in the first column; fourth column consists of either a list of possible SAPs (L, I, V) or a list of possible PTMs (N08, N09, N10, N11, N12); fifth column documents disease names, if any, associated with the modifications at the specified positions. The user may then run our script, UserDb.pl, to generate the appropriate ".seq" and ".def" files suitable for searching using RAId_DbS. More detail can be found in the help page http://www.ncbi.nlm.nih.gov/CBBresearch/qmbp/RAId_DbS/raid_help.html of RAId_DbS.