Provided by: predictprotein_1.1.08-1_all bug

NAME

       predictprotein - analyse protein sequence

SYNOPSIS

       predictprotein [--blast-processors] [--num-cpus|c] [--debug|d] [--help] [--make-file|m]
       [--makedebug] [--man] [--method] [--dryrun|n] [--numresmax] [--output-dir|o]
       [--print-ext-method-map] [--profnumresmin] [--psicexe] [--prot-name|p] [--sequence|seq|s]
       [--seqfile] [--spkeyidx] [--target]* [--version|v] [--work-dir|w]

       predictprotein [--bigblastdb] [--big80blastdb] [--pfam2db] [--pfam3db] [--prodomblastdb]
       [--prositedat] [--prositeconvdat] [--swissblastdb]

       predictprotein [--setacl|acl] [--<no>cache-merge] [--<no>force-cache-store]
       [--<no>use-cache]

DESCRIPTION

       predictprotein runs a set of protein sequnce analysis methods:

   Standard methods
       These methods are run by the default target 'all':

        Feature                Target            Extension               Man page
        -------                ------            ---------               --------
        atom mobility          profbval          profbval, profb4snap    profbval(1)
        bacterial transmem-    proftmb           proftmb, proftmbdat     proftmb(1)
         brane beta barrels
        coiled-coils           coiledcoils       coils, coils_raw        coils-wrap(1)
                                                                         ncoils(1)
        disulfide bridges      disulfinder       disulfinder             disulfinder(1)
        Gene Ontology terms    metastudent       metastudent.BPO.txt,    metastudent(1)
                                                 metastudent.CCO.txt,
                                                 metastudent.MFO.txt
        local alignment        blast             blastPsiOutTmp, chk,    blastpgp(1)
                                                 blastPsiMat,
                                                 blastPsiAli,
                                                 blastpSwissM8           blastall(1)
        local complexity       ncbi-seg          segNorm, segNormGCG     ncbi-seg(1)
        non-regular secondary  norsp             nors, sumNors           norsp(1)
         structure
        nuclear localization   predictnls        nls, nlsDat, nlsSum     predictnls(1)
        Pfam scan hmmer v2     hmm2pfam          hmm2pfam                hmm2pfam(1)
        Pfam scan hmmer v3     hmm3pfam          hmm3pfam, hmm3pfamTbl,  hmmscan(1)
                                                 hmm3pfamDomTbl
        PROSITE scan           prosite           prosite                 prosite_scan(1)
        protein-protein        profisis          isis                    profisis(1)
         interaction sites
        secondary structure,   prof              profRdb                 prof(1)
         accessibility from
         sequence profile
        secondary structure,   prof              prof1Rdb                prof(1)
         accessibility from
         single sequence
        secondary structure,   reprof            reprof                  reprof(1)
         accessibility from
         single sequence
        transmembrane          phd               phdPred, phdRdb         prof(1)
         helices
        unstructured loops     norsnet           norsnet                 norsnet(1)

   Optional methods
       These methods are non-redistributable or depend on non-redistributable software (indicated
       by '*').  You have to acquire the non-redistributable components yourself before you can
       use these methods.

       These methods are run by the target 'optional'.

        Feature                Target            Extension               Man page
        -------                ------            ---------               --------
        disordered regions     metadisorder      mdisorder               metadisorder(1)
        subcellular            loctree3          {arch,bact,euka}.lc3    loctree3(1)
                               tmhmm*            tmhmm                   n.a.
        protein-RNA,           somena            somena                  somena(1)
        protein-DNA
         interaction sites
        DNA- , RNA- and        predbind          predbind                predbind(1)
         Protein-binding
         protein and binding
         sites
        position-specific      psic*             psic, clustalngz        psic(1),
         independent counts                                              runNewPSIC(1),
         and its base multi-                                             clustalw(1)
         ple alignment
        transmembrane helices  tmhmm             tmhmm                   n.a.
                               tmseg             tmseg                   tmseg(1)
        functional regions     consurf           _consurf.grades         consurf(1)

   Resources
        Database                             Cmd line argument
        --------                             -----------------
        big (Uniprot+PDB) blast database     --bigblastdb
        big_80 (big @ 80% sequence identity  --big80blastdb
          redunancy level) blast database
        swiss blast database                 --swissblastdb
        pfam v2 database                     --pfam2db
        pfam v3 database                     --pfam3db
        prosite_convert.dat                  --prositeconvdat

       Resources for optional targets

        Database                             Cmd line argument
        --------                             -----------------
        big (Uniprot+PDB) blast database     --bigblastdb
        prosite.dat                          --prositedat
        Swiss-Prot keyword-to-accession      --spkeyidx
         'index' for loctree

   Generating Resources
       Courtesy of Wiktor Jurkowski:

        * rostlab-data-prosite_convert prosite.dat prosite_convert.dat
        * perl /usr/share/loctree/perl/keyindex4loctree.pl < keyindex.txt > keyindex_loctree.txt
        * hmmpress Pfam-A.hmm

   Output format
       Method outputs are deposited into --output-dir.  Each method has one or more file name
       extensions associated with it, see the table above.  Refer to the man page of the
       individual methods for further details.  Extensions ending with `gz' are compressed with
       gzip(1).

REFERENCES

       Rost, B., Yachdav, G., and Liu, J. (2004). The PredictProtein server. Nucleic Acids Res,
       32(Web Server issue), W321-6.

       In case you find predictprotein and the tools within useful please cite:

       * the references for PredictProtein, see above

       * the references for the tools you used, see REFERENCES on the man page of the tool

OPTIONS

       --blast-processors
           Number of processors to use, default = 1

       -c, --num-cpus
           Make jobs, default = 1

       -d, --debug
       --help
           Print a brief help message and exits.

       -m, --make-file
           make file to use, default = /usr/share/predictprotein/MakefilePP.mk

       --makedebug
           debug argument for make, see make(1)

       --man
           This documentation page

       --method
           Describes method control parameters and requests methods to run when --target is not
           all. Format example:

            --method=norsp,win=50

           * begin with the method name, e.g. `norsp'

           * list method control parameters, e.g. win=50

           Not all methods support passing control parameters in this way due to their primitive
           command line interfaces.

       -n, --dryrun
           Do not execute, just shows what is about to be run

       --numresmax
           Maximum sequence length, default: 6000. Sequences longer than this will make
           predictprotein fail with the respective error code, see ERRORS.

       -o, --output-dir
           Final location of outputfiles, required unless caching is used.

       --print-ext-method-map
           Print externsion-to-method map.  Useful as input file for consistency checkers.
           Format: <extension><tab><method>.

       --profnumresmin
           Minimum sequence length required by prof, default: 17. Sequences shorter than this
           will make predictprotein fail with the respective error code, see ERRORS.

       --psicexe
           psic wrapper executable, default: /usr/share/rost-runpsic/runNewPSIC.pl

       -p, --prot-name
           Base name of result files and protein name in - for example - FASTA files. Default =
           `query'.

           Valid names are of the character set "[[:alnum:]._-]".

       -s, --seq, --sequence
           one letter amino acid sequence input

       --seqfile
           FASTA amino acid sequence file; if `-', standard input is read

       --spkeyidx
           Swiss-Prot keyword-to-identifier 'index' file for loctree(1).

       --target=string
           Method groups to run.  Give this argument for each target you need.  Default: the
           value of `default_targets' in the configuration file; `all' if that is not given.

           Some targets of interest:

           all methods that are GPL or redistributable to non-commercial entities

           optional
               methods that do not fit into all

           Look at /usr/share/predictprotein/MakefilePP.mk for a list of targets ("Use the source
           Luke").

       -v, --version
           Print package version

       -w, --work-dir
           Working directory, optional

   Database options
       --bigblastdb
           Path to comprehensive blast database

       --big80blastdb
           Path to comprehensive blast database at 80% sequence identity redundancy level

       --pfam2db
           Pfam v2 database, e.g. Pfam_ls

       --pfam3db
           Pfam v3 database, e.g. Pfam-A.hmm

       --prodomblastdb
           Obsolete.  This argument is kept only to maintain compatibility with older versions.

       --prositedat
           Path to `prosite.dat' file, see
           <https://rostlab.org/owiki/index.php/Packages#Resource_definitions>

       --prositeconvdat
           Path to `prosite_convert.dat' file, see
           <https://rostlab.org/owiki/index.php/Packages#Resource_definitions>

       --swissblastdb
           Path to SwissProt blast database

   Cache related options
       --acl, --setacl
           Set access control lists.  Access control lists are set only in case results are
           stored in the cache.  This option is ineffective otherwise.  All previous ACLs are
           lost - no merging.  The read bit controls browsability of results. Other bits are not
           used. E.g.

            u:lkajan:4,u:gyachdav:4,g:lkajan:4,o::0

       --cache-merge
       --nocache-merge
           Merge/do not merge results into cache.  --cache-merge reuses results already in cache;
           this turns --use-cache on automatically.  --cache-merge is incompatible with
           --force-cache-store.

           --nocache-merge is the default UNLESS

           ·   --use-cache is on and

           ·   --noforce-cache-store is in effect and

           ·   --target is used and

           ·   the cache is not empty

           --cache-merge is silently ignored in case the cache is empty.

       --force-cache-store
       --noforce-cache-store
           Enable/disable forcing storage of results into cache.  Implies --use-cache.  Default:
           --noforce-cache-store

           With --noforce-cache-store when predictprotein finds cached results it simply fetches
           them from the cache and does no processing (even if the results are incomplete).  With
           --force-cache-store predictprotein does not fetch anything from the cache but does
           store the results, completely replacing what was cached.

           --force-cache-store is incompatible with --cache-merge.

       --use-cache
       --nouse-cache
           Use/do not use cache for predictprotein results.  Default: --nouse-cache.

           Option `use_cache' may be given in configuration files to override default.

ERRORS

       253 Sequence is too long, see --numresmax

       254 Sequence is too short, shorter than minimum length required by prof. See
           --profnumresmin.

EXAMPLES

        predictprotein --seqfile /usr/share/doc/predictprotein/examples/tquick.fasta --output-dir /tmp/pp

        predictprotein --seqfile /usr/share/doc/predictprotein/examples/tquick.fasta --output-dir /tmp/pp --target query.profRdb --target loctree3

        predictprotein --seqfile /usr/share/doc/predictprotein/examples/tquick.fasta --method=norsp,win=100 --output-dir /tmp/pp

   Cache examples
       Store results in cache, do not care about storing files in --output-dir:
            predictprotein --seqfile /usr/share/doc/predictprotein/examples/tquick.fasta --method=norsp,win=100 --use-cache --setacl g:rostlab:7

       If not in cache store, otherwise fetch results from cache into --output-dir:
            predictprotein --seqfile /usr/share/doc/predictprotein/examples/tquick.fasta --method=norsp,win=100 --use-cache --setacl g:rostlab:7 --output-dir /tmp/pp

ENVIRONMENT

       PREDICTPROTEINCONF
           Location of predictproteinrc configuration file to use, overriding other configuration
           files

FILES

       /usr/share/predictprotein/predictproteinrc.default
           Default configuration file. See this file for a description of the parameters.

       /etc/predictproteinrc
           System configuration file overriding values in
           /usr/share/predictprotein/predictproteinrc.default

       ~/.predictproteinrc
           User configuration file overriding values in /etc/predictproteinrc

NOTES

   Popularity Contest
       The pp-popularity-contest package included with this image sets up a cron job that will
       periodically anonymously submit to the Rost Lab developers statistics about the most used
       Rost Lab packages on this system.

       This information helps us making decisions such as which packages should receive high
       priority when fixing bugs.  It also helps us decide which packages should receive funding
       for further development and support.  This information is also very important when the
       Rost Lab applies for funding.

       Without the funding we receive based on the usage statistics you volunteer none of the
       packages on this image could be made available to you at no cost.

       In case you do not wish to participate in the popularity contest please remove the pp-
       popularity-contest package.

AUTHOR

       Burkhard Rost, Antoine de Daruvar, Jinfeng Liu, Guy Yachdav, Laszlo Kajan

SEE ALSO

       ppc_store(1), ppc_fetch(1), ppqsub(1)