Provided by: freecontact_1.0.21-7_amd64 bug

NAME

       freecontact - fast protein contact predictor

SYNOPSIS

       freecontact [OPTION]

       freecontact --parprof [evfold|psicov|psicov-sd] < alignment.aln > contacts.out

       /usr/share/freecontact/a2m2aln --query '^RASH_HUMAN/(\d+)' < alignment.fa | freecontact
       --parprof evfold > contacts.out

       freecontact --ali=ALIFILE --apply-gapth=BOOL --clustpc=NUM --density=NUM --cov20=BOOL
       --estimate-ivcov=BOOL --gapth=NUM --icme-timeout=NUM --input-format=[flat|xml]
       --mincontsep=NUM --output-format=[evfold|pfrmat_rr|bioxsd] --pseudocnt=NUM
       --pscount-weight=NUM --rho=NUM --threads=NUM --veczw=BOOL

       freecontact --help --debug --quiet --version

DESCRIPTION

       FreeContact is a protein residue contact predictor optimized for speed.  FreeContact can
       function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of
       DS. Marks et al. (2011) [1], and PSICOV of D. Jones et al. (2011) [2].

       FreeContact is accelerated by a combination of vector instructions, multiple threads, and
       faster implementation of key parts.  Depending on the alignment, 8-fold or higher speedups
       are possible.

       A sufficiently large alignment is required for meaningful results.  As a minimum, an
       alignment with an effective (after-weighting) sequence count bigger than the length of the
       query sequence should be used. Alignments with tens of thousands of (effective) sequences
       are considered good input.

       jackhmmer(1) or hhblits(1) can be used to generate the alignments, for example.

       [1] PLoS One. 2011;6(12):e28766. doi: 10.1371/journal.pone.0028766. Epub 2011 Dec 7.
       Protein 3D structure computed from evolutionary sequence variation.  Marks DS, Colwell LJ,
       Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C.

       [2] Bioinformatics. 2012 Jan 15;28(2):184-90. Epub 2011 Nov 17.  PSICOV: precise
       structural contact prediction using sparse inverse covariance estimation on large multiple
       sequence alignments.  Jones DT, Buchan DW, Cozzetto D, Pontil M.

   Input
       The following formats are supported:

       flat
           The following simple input file format is used:

            # querystart=5
            # query=QUERYwithinsertionSEQUENCEWITHNOGAPSORINSERTIONS
            QUERYSEQUENCEWITHNOGAPSORINSERTIONS
            -ALIGNED---SEQUENCE--WITH-GAPS-----
            ANOTHER-ALIGNED------------SEQUENCE

           The '#' header lines are optional. Header lines are used to calculate contact residue
           numbers and to look up respective query residues for certain output formats.

           If no query is defined, the first sequence in the alignment is used as the query
           sequence.  The query sequence must not contain gaps in the alignment.

           All alignment rows must be the same length, and may contain only
           [ABCDEFGHIJKLMNOPQRSTUVWXYZ-]. [B] is mapped to [D], [Z] is mapped to [E], [JOUX] are
           mapped to [X].  [X] matches only itself for the entire program.

           A2M input alignments can be converted to the above format using
           /usr/share/freecontact/a2m2aln.  a2m2aln can be used to pipe the alignment directly
           into freecontact.

       xml XML document with one <fc:alignment xmlns:fc="http://rostlab.org/freecontact/xsd"/>
           element, defined in the FreeContact schema [4] derived from BioXSD [5].

           Example: /usr/share/doc/freecontact/examples/PF00071_v25_1000.xml.

   Output
       The original EVfold-mfDCA or PSICOV output format is used by default when the respective
       parameter profile is selected.

       evfold (EVfold-mfDCA)
            5 K 6 L 0.332129 3.59798
            | | | | |        + corrected norm (CN) contact score
            | | | | + mutual information (MI) score
            | | | + contact amino acid residue code
            | | + contact residue number
            | + contact amino acid residue code
            + contact residue number

           Contacts are sorted on residue number.

       pfrmat_rr (PSICOV)
           CASP residue-residue separation prediction (PFRMAT RR) format [3]:

            55 67 0 8 10.840280
            |  |  | | + contact score
            |  |  +-+ range [Å] of Cb-Cb distance predicted for the residue pair
            |  |      (C-alpha for glycines)
            |  |      These two fields are invariant in the output.
            |  + contact residue number
            + contact residue number

           Contacts are sorted on score, descending.

           [3] <http://predictioncenter.org/casp10/index.cgi?page=format>

       bioxsd
           XML document with one <fc:contactMap xmlns:fc="http://rostlab.org/freecontact/xsd"/>
           element, defined in the FreeContact schema [4] derived from BioXSD [5].

           Example: /usr/share/doc/freecontact/examples/PF00071_v25_1000.evfold.50.xml.

           Note: as BioXSD is under active development in collaboration with FreeContact, the
           FreeContact schema may actually be derived from a version not yet available at [5].

           [4] <file:///usr/share/freecontact/freecontact.xsd>

           [5] <http://bioxsd.org>

       The output may not list all possible contacts.

REFERENCES

           Submitted.  FreeContact: fast and free direct residue-residue contact prediction.
           Kaján L, Sustik MA, Marks DS, Hopf TA, Kalaš M, Rost B.

OPTIONS

       -a [ --threads ] arg
           Threads to use [0-). 0 means as many as cores.

       --apply-gapth arg
           When true, exclude residue columns and rows with a weighted gap frequency > --gapth
           from the covariance matrix [Boolean].

       -c [ --clustpc ] arg
           BLOSUM clustering percentage [0-100].

       --cov20 arg
           If true, leave one amino acid off the covariance matrix, making it non-overdetermined
           [Boolean].

       -d [ --density ] arg
           Target precision matrix density [0-1]. Set 0 to not control density.

       --debug
           Turn on debugging.

       --estimate-ivcov arg
           Use inverse covariance matrix estimation instead of matrix inversion [Boolean].

       -f [ --ali ] arg (=-)
           Alignment file [path]. If '-', standard input. Default: '-'.

       -g [ --gapth ] arg
           Weighted gap frequency threshold (0-1].

       -h [ --help ]
           Produce this help message.

       -i [ --input-format ] arg (=flat)
           Input format [flat|xml].

       --icme-timeout arg (=1800)
           Inverse covariance matrix estimation timeout in seconds [0-). Applied to each iversion
           call independently. If a timeout occurs, the program exits with status 2.

       --mincontsep arg
           Minimum sequence-wise contacting residue pair separation given in amino acids as
           (j-i>=arg). 1 for adjacent residues. [1-).

       -o [ --output-format ] arg
           Output format [evfold|pfrmat_rr|bioxsd].

       --parprof arg (=default)
           Parameter profile (optional) [default|evfold|psicov].  The default profile is evfold.

           Command line arguments can be used to override profile values.

           evfold
               Triggers EVfold-mfDCA [1] compatibility mode.

           psicov
               Triggers PSICOV [2] compatibility mode.

           psicov-sd
               Triggers PSICOV [2] sensible default mode: fixed default rho, no density control.

       -w [ --pscount-weight ] arg
           Pseudocount weight [0-1].

       -p [ --pseudocnt ] arg
           Pseudocount [0-).

       --pep
           Print effective parameters on standard error.  Use this option to see what parameters
           freecontact(1) is run with in detail.  This is especially useful when the --parprof
           option is used in combination with other options.

       --rho arg
           Initial value of Glasso regularization parameter [0-).  If negative, choose value
           automatically.

       --quiet arg (=0)
           Print nothing but error messages on standard error.  Does not affect --debug.

       --veczw arg
           Use vectorized sequence weighting when available [Boolean].

       --version
           Print version.

EXIT STATUS

       0   No error - success.

       1   Unspecified error.

       2   A timeout (see --icme-timeout) occurred.

EXAMPLES

        /usr/share/freecontact/a2m2aln --query '^RASH_HUMAN/(\d+)' < '/usr/share/doc/freecontact/examples/PF00071_v25_1000.fa' | \
         freecontact --parprof evfold > PF00071_v25_1000.evfold

        freecontact --parprof evfold -i xml -o bioxsd < '/usr/share/doc/freecontact/examples/PF00071_v25_1000.xml' > PF00071_v25_1000.evfold.xml

        freecontact --parprof psicov < /usr/share/doc/freecontact/examples/demo_1000.aln > demo_1000.psicov

NOTES

       For optimal performance, use the Automatically Tuned Linear Algebra Software (ATLAS)
       library compiled on the machine where freecontact is run.

AUTHOR

       László Kaján <lkajan@rostlab.org>

SEE ALSO

       jackhmmer(1), hhblits(1), blastpgp(1)