A Flag-tag can be used in many different assays that require recognition by an antibody. If there is no antibody against the studied protein, adding a FLAG-tag to this protein allows following the protein with an antibody against the Flag sequence. Examples are cellular localization studies by immunofluorescence or detection by SDS PAGE protein electrophoresis.
The peptide sequence of the FLAG-tag is as follows: N-DYKDDDDK-C. It can be used in conjunction with other affinity tags for example a polyhistidine tag (His-tag), HA-tag or myc-tag. It can be fused to the C-terminus and the N-terminus of a protein. However, one has to be careful, that some commercially available antibodies recognize the epitope only in certain positions, e.g. exclusively N-terminal; in this case a leading Met followed by the FLAG-sequence is mandatory.