freecontact - Online in the Cloud

PROGRAM:

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.

Use freecontact online using onworks.net services