There are two types of databases used by the FFAS server. Sequence-pool database used to calculate sequence profiles, and template databases searched for homologues.
Sequence-sequence comparison method. The blast results available through blast links on the FFAS03 results page contain the homologues found by BLAST method in the template database(s) of sequences. Please see BLAST tutorial for more information about BLAST.
Iterative profile-sequence comparison method. On the FFAS03 server PSI-BLAST is used to search the sequence-pool database. The results of PSI-BLAST stored on the FFAS server are the multiple sequence alignments from 5 PSI-BLAST iterations used by FFAS to calculate sequence profiles. Please see PSI-BLAST tutorial for more information about PSI-BLAST.
A profile-sequence comparison method. A method of using PSI-BLAST optimized for searches in small sequence databases. PDB-BLAST searches the template database(s) using a profile generated by PSI-BLAST from sequence-pool database. Such procedure was shown to significantly improve the effectiveness of the search. The PDB-BLAST search consists of two PSI-BLAST runs. The first run searches sequence-pool database to derive a profile of a query sequence. Then this profile is used to search template database(s) such as PDB sequences Please see publication about PDB-BLAST for more information about PDB-BLAST.
A profile-profile comparison method. It calculates sequence profiles for both query sequence(s) and the sequences from the template databases. Subsequently, sequence profiles are aligned using dynamic programming algorithm. All the profiles from the template databases are precalculated and stored on the server. Please see publications about FFAS for more information.