Principle of the FTHOM algorithm (H. Hegyi and S. Pongor, Comput. Applic. Biosci.,9, 371-372, 1992.)

This scoring is repeated for each alignment in the BLAST output and a sumary list is presented in terms of domain homologies, ranked by score. The below example is the analysis of the human C1S light chain, a serin protease which has a propetide removed by proteolysis.

                          Feature                 FT    Score
                           name                  freq

                       DOMAIN SERINE PROTEASE.    28    6697
                             DOMAIN CATALYTIC.     1     301
                         SIMILAR WITH TRYPSIN.     1     269
                            DOMAIN BETA CHAIN.     1     256
                       DOMAIN SERINE-PROTEASE.     1     122
                             DOMAIN SEGMENT A.     1     112
                            DOMAIN SEGMENT B2.     1      72
                            DOMAIN SEGMENT B1.     1      62
                             DOMAIN SEGMENT C.     1      40
                          PROPEP PROLINE-RICH.     3      27
 SITE MAY BE REMOVED BUT IS NOT NECESSARY FOR      1      19
                                   ACTIVATION.
                                      CA_BIND.     1       8
            SITE CLEAVAGE SITE (BY FACTOR XA).     3       3
SITE CLEAVAGE (BY FACTOR XIA) (BY SIMILARITY).     2       2
                SITE CLEAVAGE (BY FACTOR XIA).     2       2
                            BINDING SUBSTRATE.     2       2
                 SITE CLEAVAGE (BY FACTOR XA).     1       1
                    PROPEP ACTIVATION PEPTIDE.     1       1
      SITE CLEAVAGE BY FACTOR XA, FACTOR XIIA,     1       1
                SITE THROMBIN ACTIVATION SITE.     1       1

The colors indicate that the different domain names were used in the early version of Swiss-Prot used for the search. Since 1992, standardization of domain names started within the SBASE project, and the standard names greatly simplify the output:

With SBASE 3.0 standard names

                            SERINE-PROTEASE.    36 7958
                            PROCESSING-SITE.    14   40
                        PROPEP PROLINE-RICH.     3   27
                                 CA-BINDING.     1    8

Note that even a short feature, like a proteolitic procesing site of 1-2 amino acids can be noticed with this simple procedure. FTHOM is part of the domain server (domain@hubi.abc.hu)