predictprotein1

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).

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.

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

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.