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