The FFAS03 server provides an interface to the third generation of the profile-profile alignment and fold recognition algorithm FFAS. Profile-profile alignments utilize information present in sequences of homologous proteins to amplify the sequence conservation pattern defining the family resulting in detection of remote homologies beyond the reach of other sequence comparison methods. Input into the FFAS03 server is a protein sequence provided by the user. From the sequence a profile is generated which is then compared to several databases of sequence profiles of proteins and domains from public databases, such as PDB, COG, PFAM, and SCOP. The latest structural and sequence information is updated in the FFAS03 template databases. In addition, FFAS03 server provides access to comparative modeling tools. Registration not required.