133 lines
5.6 KiB
Plaintext
133 lines
5.6 KiB
Plaintext
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Preparing the PROSITE protein motif library for use by
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the Staden programs
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Introduction
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A library of protein motifs (in our terminology, because
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they include variable gaps, some would be called patterns) has
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recently become available from Amos Bairoch,Departement de
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Biochimie Medicale,University of Geneva Currently it contains 317
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patterns/motifs and arrives on tape or cdrom in two files: a .dat
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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
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PROSITE library for use by our programs.
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Three programs need to be run SPLITP1, SPLITP2, and
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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.
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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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Each entry has an accession number (here PS00197), a
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pattern definition (here C-x(1,2)-[STA]-x(2)-C-[STA]-{P}-C) and a
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documentation file cross reference (here PDOC00175). This
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pattern means: C, gap of 1 or 2, any of STA, gap of 2, C, any of
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STA, not P, C.
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We need to convert all of these patterns into our pattern
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definitions (as membership of a set, with the appopriate gap
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ranges) and write each into a separate pattern file with
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corresponding "membership of a set" weight matrices. Each pattern
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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
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PS00197.WTSA and PS00197.WTSB): two are needed because of the
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variable gap.
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In addition we can optionally split the .dat and .doc
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files into separate files, one for each entry, with names
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accession_number.dat and accession_number.doc. Also we create an
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index for the library prosite.lis, which gives a one line
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description of each pattern, and ends with the pattern file and
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documentation file numbers. The start of the file is shown below.
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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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So the name of the pattern file for Glycosaminoglycan attachment
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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
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patterns in the library.
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To use the complete PROSITE library from program pip,
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select "pattern searcher" and choose the option "use file of
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pattern file names", and give the file name prosite.nam). For any
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matches found, the accession number and pattern title will be
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displayed.
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Running the conversion programs
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Only SPLITP3 is necessary for using the library. The
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others programs only make the original files marginally easier to
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browse through and produce an index.
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SPLITP1 splits the prosite.dat file to create a separate
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file for each entry. Each file is automatically named
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PSentry_number.dat. In addition it creates an index for the
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library (see above).
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SPLITP2 performs the same operation for the Prosite.doc
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file, except that no index is created. Files are named
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PSentry_number.doc.
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SPLITP3 creates a separate pattern file and weight matrix
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files for each prosite entry from the file prosite.dat. Pattern
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files are named PSentry_number.pat, weight matrix files
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PSentry_number.wtsa, Psentry_number.wtsb, etc. The pattern title
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is the one line description of the motif. SPLITP3 also creates a
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file of file names. Notice that it will ask for a path name so
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that the path can be included in the file of file names. This is
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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
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solution, and anybody could now create their own set of
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interesting patterns for screening, or a subset of prosite.nam,
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etc.
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Note that 5 of the bairoch motifs contained the symbols >
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or < which means that the motifs must appear exactly at the N or
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C termini of the sequences. Currently our methods have no
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mechanism for such definitions and, for example KDEL motifs, will
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be permitted to occur anywhere throughout a sequence.
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Also, of course, the library does not have to be used
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solely for performing mass screenings: each individual entry can
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be used as a single pattern by giving the name of its .pat file -
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eg pathname/ps00002.pat In addition more sophisticated users will
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wish to copy pattern files and weight matrices into their own
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directories and modify them. For example the cutoff scores are
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probably chosen to be quite high in order to reduce the number of
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false positives, and some users might wish to lower them.
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