PROFILES DATABASE

PRINTS, BLOCKS, PROSITE and IDENTIFY are motif based databases.
An alternative philosophy to the motif based approach of protein family characterization is that the variable sequences in between the conserved motifs are also valuable in protein family characterisation.
A 'complete sequence alignment' is used as the discriminator in PROFILES Database as blocks are the discriminators in BLOCKS database.
Profile is the discriminator in the PROFILES Database . A profile is also called a weighted matrix because it is weighted to indicate where insertions and deletions are allowed, where the most conserved regions are present etc.,
Profiles provide a sensitive means of detecting distant relationships, where only few residues are well conserved; in these circumstances regular expressions cannot provide good discrimination.
These profiles are the bases of the PROFILES Database.
The PROFILES Database is developed at the Swiss Institute of experimental cancer research in Lausanne.
Each Profile has seperate data and family annotation files as PROSITE has separate data and documentation files.

STRUCTURE OF PROSITE PROFILE ENTRIES:

ID SH3; MATRIX
AC PS50002
DT NOV-1995 (CREATED); NOV-1995(DATA UPDATED); NOV-1995(INFO UPDATED)

DE Src homology 3 (SH3) domain profile.
MA
MA
.
.
.
MA
MA
MA
MA
MA
MA
MA
MA
.
.
.
.

The above figure illustrates a part of the profile used to characterize the SH3 domain.

The Structure of a profile entry is based on PROSITE but with obvious differences.
The structure has following lines :-
1) ID Line : Identification line
2) Accession number line (AC Line) : The accession number doesnt change and it remains the same as long as the entry exists in the database. It is of the form PS00000.
3) DT Line : Date Line : Date Line follows the AC line. It has information on when the entry is created and when its last updated.
4) DE line: It five the description about the Profile.
5) MA line follows the description line. MA line means Matrix Lines. The PA(Pattern) lines are replaced by the Matrix lines. MA lines tests various parameter specifications used to derive and describe the profile. They include details if the alphabet used (i.e, whether nucleic acid {AGCT} or aminoacid {ABCD......}), LENGTH OF THE pROFILE ETC.

PROFILE Database id accessible through ISREC Web Server