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Preparing the PROSITE protein motif library for use by the Staden programs
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Introduction
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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.
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Three programs need to be run SPLITP1, SPLITP2, and SPLITP3.
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Outline of the PROSITE files
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 A typical entry in the .dat file is shown below.
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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;
//
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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.
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  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. 
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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.
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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

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So the name of the pattern file for Glycosaminoglycan attachment site is 
PS00002.PAT, and for the documentation file PDOC00002.DOC
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Finally we
create a file of file names for all the patterns in the library.
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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.

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Running the conversion programs
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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.
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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).
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SPLITP2 performs the same operation for the Prosite.doc file, except that 
no index is created. Files are named PSentry_number.doc.
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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.
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Notes
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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.
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   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.

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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.