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 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.