Preparing the PROSITE protein motif library for use by
the Staden programs
Introduction
A library of protein motifs (in our terminology, because
they include variable gaps, some would be called patterns) has
recently become available from Amos Bairoch,Departement de
Biochimie Medicale,University of Geneva Currently it contains 317
patterns/motifs and arrives on tape or cdrom in two files: a .dat
file and a .doc file. There is also a user documentation file
prosite.usr. Here I outline what is required to prepare the
PROSITE library for use by our programs.
Three programs need to be run SPLITP1, SPLITP2, and
SPLITP3.
Outline of the PROSITE files
A typical entry in the .dat file is shown below.
ID 2FE2S_FERREDOXIN; PATTERN.
AC PS00197;
DT APR-1990 (CREATED); APR-1990 (DATA UPDATE); APR-1990 (INFO UPDATE).
DE 2Fe-2S ferredoxins, iron-sulfur binding region signature.
PA C-x(1,2)-[STA]-x(2)-C-[STA]-{P}-C.
NR /RELEASE=14,15409;
NR /TOTAL=69(69); /POSITIVE=63(63); /UNKNOWN=0(0); /FALSE_POS=6(6);
NR /FALSE_NEG=5(5);
CC /TAXO-RANGE=A?EP?; /MAX-REPEAT=1;
CC /SITE=1,iron_sulfur; /SITE=5,iron_sulfur; /SITE=8,iron_sulfur;
DR P15788, FER$APHHA , T; P00250, FER$APHSA , T; P00223, FER$ARCLA , T;
DR P00227, FER$BRANA , T; P07838, FER$BRYMA , T; P13106, FER$BUMFI , T;
DR P00247, FER$CHLFR , T; P07839, FER$CHLRE , T; P00222, FER$COLES , T;
DO PDOC00175;
//
Each entry has an accession number (here PS00197), a
pattern definition (here C-x(1,2)-[STA]-x(2)-C-[STA]-{P}-C) and a
documentation file cross reference (here PDOC00175). This
pattern means: C, gap of 1 or 2, any of STA, gap of 2, C, any of
STA, not P, C.
We need to convert all of these patterns into our pattern
definitions (as membership of a set, with the appopriate gap
ranges) and write each into a separate pattern file with
corresponding "membership of a set" weight matrices. Each pattern
file is named accession_number.pat (here PS00197.PAT). The
corresponding matrix files are accession_number.wtsa,
accession_number.wtsb, etc for however many are needed (here
PS00197.WTSA and PS00197.WTSB): two are needed because of the
variable gap.
In addition we can optionally split the .dat and .doc
files into separate files, one for each entry, with names
accession_number.dat and accession_number.doc. Also we create an
index for the library prosite.lis, which gives a one line
description of each pattern, and ends with the pattern file and
documentation file numbers. The start of the file is shown below.
N-glycosylation site. 00001,00001
Glycosaminoglycan attachment site. 00002,00002
Tyrosine sulfatation site. 00003,00003
cAMP- and cGMP-dependent protein kinase phosphorylation site. 00004,00004
So the name of the pattern file for Glycosaminoglycan attachment
site is PS00002.PAT, and for the documentation file PDOC00002.DOC
Finally we create a file of file names for all the
patterns in the library.
To use the complete PROSITE library from program pip,
select "pattern searcher" and choose the option "use file of
pattern file names", and give the file name prosite.nam). For any
matches found, the accession number and pattern title will be
displayed.
Running the conversion programs
Only SPLITP3 is necessary for using the library. The
others programs only make the original files marginally easier to
browse through and produce an index.
SPLITP1 splits the prosite.dat file to create a separate
file for each entry. Each file is automatically named
PSentry_number.dat. In addition it creates an index for the
library (see above).
SPLITP2 performs the same operation for the Prosite.doc
file, except that no index is created. Files are named
PSentry_number.doc.
SPLITP3 creates a separate pattern file and weight matrix
files for each prosite entry from the file prosite.dat. Pattern
files are named PSentry_number.pat, weight matrix files
PSentry_number.wtsa, Psentry_number.wtsb, etc. The pattern title
is the one line description of the motif. SPLITP3 also creates a
file of file names. Notice that it will ask for a path name so
that the path can be included in the file of file names. This is
the path to the directory in which the pattern files are stored.
Notes
Obviously the use of files of file names is a general
solution, and anybody could now create their own set of
interesting patterns for screening, or a subset of prosite.nam,
etc.
Note that 5 of the bairoch motifs contained the symbols >
or < which means that the motifs must appear exactly at the N or
C termini of the sequences. Currently our methods have no
mechanism for such definitions and, for example KDEL motifs, will
be permitted to occur anywhere throughout a sequence.
Also, of course, the library does not have to be used
solely for performing mass screenings: each individual entry can
be used as a single pattern by giving the name of its .pat file -
eg pathname/ps00002.pat In addition more sophisticated users will
wish to copy pattern files and weight matrices into their own
directories and modify them. For example the cutoff scores are
probably chosen to be quite high in order to reduce the number of
false positives, and some users might wish to lower them.