.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "FREECONTACT 1" .TH FREECONTACT 1 "2021-04-07" "1.0.21" "User Commands" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" freecontact \- fast protein contact predictor .SH "SYNOPSIS" .IX Header "SYNOPSIS" freecontact [\s-1OPTION\s0] .PP freecontact \-\-parprof [evfold|psicov|psicov\-sd] < alignment.aln > contacts.out .PP /usr/share/freecontact/a2m2aln \-\-query '^RASH_HUMAN/(\ed+)' < alignment.fa | freecontact \-\-parprof evfold > contacts.out .PP freecontact \-\-ali=\fI\s-1ALIFILE\s0\fR \-\-apply\-gapth=\fI\s-1BOOL\s0\fR \-\-clustpc=\fI\s-1NUM\s0\fR \-\-density=\fI\s-1NUM\s0\fR \-\-cov20=\fI\s-1BOOL\s0\fR \-\-estimate\-ivcov=\fI\s-1BOOL\s0\fR \-\-gapth=\fI\s-1NUM\s0\fR \-\-icme\-timeout=\fI\s-1NUM\s0\fR \-\-input\-format=\fI[flat|xml]\fR \-\-mincontsep=\fI\s-1NUM\s0\fR \-\-output\-format=\fI[evfold|pfrmat_rr|bioxsd]\fR \-\-pseudocnt=\fI\s-1NUM\s0\fR \-\-pscount\-weight=\fI\s-1NUM\s0\fR \-\-rho=\fI\s-1NUM\s0\fR \-\-threads=\fI\s-1NUM\s0\fR \-\-veczw=\fI\s-1BOOL\s0\fR .PP freecontact \-\-help \-\-debug \-\-quiet \-\-version .SH "DESCRIPTION" .IX Header "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 \s-1DS.\s0 Marks et al. (2011) [1], and \&\s-1PSICOV\s0 of D. Jones et al. (2011) [2]. .PP 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. .PP 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. .PP \&\fBjackhmmer\fR\|(1) or \fBhhblits\fR\|(1) can be used to generate the alignments, for example. .PP [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 \s-1DS,\s0 Colwell \s-1LJ,\s0 Sheridan R, Hopf \s-1TA,\s0 Pagnani A, Zecchina R, Sander C. .PP [2] Bioinformatics. 2012 Jan 15;28(2):184\-90. Epub 2011 Nov 17. \s-1PSICOV:\s0 precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Jones \s-1DT,\s0 Buchan \s-1DW,\s0 Cozzetto D, Pontil M. .SS "Input" .IX Subsection "Input" The following formats are supported: .IP "\fIflat\fR" 4 .IX Item "flat" The following simple input file format is used: .Sp .Vb 5 \& # querystart=5 \& # query=QUERYwithinsertionSEQUENCEWITHNOGAPSORINSERTIONS \& QUERYSEQUENCEWITHNOGAPSORINSERTIONS \& \-ALIGNED\-\-\-SEQUENCE\-\-WITH\-GAPS\-\-\-\-\- \& ANOTHER\-ALIGNED\-\-\-\-\-\-\-\-\-\-\-\-SEQUENCE .Ve .Sp 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. .Sp 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. .Sp All alignment rows must be the same length, and may contain only [\s-1ABCDEFGHIJKLMNOPQRSTUVWXYZ\-\s0]. [B] is mapped to [D], [Z] is mapped to [E], [\s-1JOUX\s0] are mapped to [X]. [X] matches only itself for the entire program. .Sp A2M input alignments can be converted to the above format using \fI/usr/share/freecontact/a2m2aln\fR. a2m2aln can be used to pipe the alignment directly into freecontact. .IP "\fIxml\fR" 4 .IX Item "xml" \&\s-1XML\s0 document with one element, defined in the FreeContact schema [4] derived from BioXSD [5]. .Sp Example: \fI/usr/share/doc/freecontact/examples/PF00071_v25_1000.xml\fR. .SS "Output" .IX Subsection "Output" The original EVfold-mfDCA or \s-1PSICOV\s0 output format is used by default when the respective parameter profile is selected. .IP "\fIevfold\fR (EVfold-mfDCA)" 4 .IX Item "evfold (EVfold-mfDCA)" .Vb 7 \& 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 .Ve .Sp Contacts are sorted on residue number. .IP "\fIpfrmat_rr\fR (\s-1PSICOV\s0)" 4 .IX Item "pfrmat_rr (PSICOV)" \&\s-1CASP\s0 residue-residue separation prediction (\s-1PFRMAT RR\s0) format [3]: .Sp .Vb 7 \& 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 .Ve .Sp Contacts are sorted on score, descending. .Sp [3] .IP "\fIbioxsd\fR" 4 .IX Item "bioxsd" \&\s-1XML\s0 document with one element, defined in the FreeContact schema [4] derived from BioXSD [5]. .Sp Example: \fI/usr/share/doc/freecontact/examples/PF00071_v25_1000.evfold.50.xml\fR. .Sp 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]. .Sp [4] .Sp [5] .PP The output may not list all possible contacts. .SH "REFERENCES" .IX Header "REFERENCES" .RS 4 Submitted. FreeContact: fast and free direct residue-residue contact prediction. Kaján L, Sustik \s-1MA,\s0 Marks \s-1DS,\s0 Hopf \s-1TA,\s0 Kalaš M, Rost B. .RE .SH "OPTIONS" .IX Header "OPTIONS" .IP "\-a [ \-\-threads ] arg" 4 .IX Item "-a [ --threads ] arg" Threads to use [0\-). 0 means as many as cores. .IP "\-\-apply\-gapth arg" 4 .IX Item "--apply-gapth arg" When true, exclude residue columns and rows with a weighted gap frequency > \fB\-\-gapth\fR from the covariance matrix [Boolean]. .IP "\-c [ \-\-clustpc ] arg" 4 .IX Item "-c [ --clustpc ] arg" \&\s-1BLOSUM\s0 clustering percentage [0\-100]. .IP "\-\-cov20 arg" 4 .IX Item "--cov20 arg" If true, leave one amino acid off the covariance matrix, making it non-overdetermined [Boolean]. .IP "\-d [ \-\-density ] arg" 4 .IX Item "-d [ --density ] arg" Target precision matrix density [0\-1]. Set \fI0\fR to not control density. .IP "\-\-debug" 4 .IX Item "--debug" Turn on debugging. .IP "\-\-estimate\-ivcov arg" 4 .IX Item "--estimate-ivcov arg" Use inverse covariance matrix estimation instead of matrix inversion [Boolean]. .IP "\-f [ \-\-ali ] arg (=\-)" 4 .IX Item "-f [ --ali ] arg (=-)" Alignment file [path]. If '\-', standard input. Default: '\-'. .IP "\-g [ \-\-gapth ] arg" 4 .IX Item "-g [ --gapth ] arg" Weighted gap frequency threshold (0\-1]. .IP "\-h [ \-\-help ]" 4 .IX Item "-h [ --help ]" Produce this help message. .IP "\-i [ \-\-input\-format ] arg (=flat)" 4 .IX Item "-i [ --input-format ] arg (=flat)" Input format [flat|xml]. .IP "\-\-icme\-timeout arg (=1800)" 4 .IX Item "--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 \fI2\fR. .IP "\-\-mincontsep arg" 4 .IX Item "--mincontsep arg" Minimum sequence-wise contacting residue pair separation given in amino acids as (j\-i>=arg). \fI1\fR for adjacent residues. [1\-). .IP "\-o [ \-\-output\-format ] arg" 4 .IX Item "-o [ --output-format ] arg" Output format [evfold|pfrmat_rr|bioxsd]. .IP "\-\-parprof arg (=default)" 4 .IX Item "--parprof arg (=default)" Parameter profile (optional) [default|evfold|psicov]. The default profile is \fIevfold\fR. .Sp Command line arguments can be used to override profile values. .RS 4 .IP "evfold" 4 .IX Item "evfold" Triggers EVfold-mfDCA [1] compatibility mode. .IP "psicov" 4 .IX Item "psicov" Triggers \s-1PSICOV\s0 [2] compatibility mode. .IP "psicov-sd" 4 .IX Item "psicov-sd" Triggers \s-1PSICOV\s0 [2] sensible default mode: fixed default rho, no density control. .RE .RS 4 .RE .IP "\-w [ \-\-pscount\-weight ] arg" 4 .IX Item "-w [ --pscount-weight ] arg" Pseudocount weight [0\-1]. .IP "\-p [ \-\-pseudocnt ] arg" 4 .IX Item "-p [ --pseudocnt ] arg" Pseudocount [0\-). .IP "\-\-pep" 4 .IX Item "--pep" Print effective parameters on standard error. Use this option to see what parameters \fBfreecontact\fR\|(1) is run with in detail. This is especially useful when the \fB\-\-parprof\fR option is used in combination with other options. .IP "\-\-rho arg" 4 .IX Item "--rho arg" Initial value of Glasso regularization parameter [0\-). If negative, choose value automatically. .IP "\-\-quiet arg (=0)" 4 .IX Item "--quiet arg (=0)" Print nothing but error messages on standard error. Does not affect \fB\-\-debug\fR. .IP "\-\-veczw arg" 4 .IX Item "--veczw arg" Use vectorized sequence weighting when available [Boolean]. .IP "\-\-version" 4 .IX Item "--version" Print version. .SH "EXIT STATUS" .IX Header "EXIT STATUS" .IP "\fI0\fR" 4 .IX Item "0" No error \- success. .IP "\fI1\fR" 4 .IX Item "1" Unspecified error. .IP "\fI2\fR" 4 .IX Item "2" A timeout (see \fB\-\-icme\-timeout\fR) occurred. .SH "EXAMPLES" .IX Header "EXAMPLES" .Vb 2 \& /usr/share/freecontact/a2m2aln \-\-query \*(Aq^RASH_HUMAN/(\ed+)\*(Aq < \*(Aq/usr/share/doc/freecontact/examples/PF00071_v25_1000.fa\*(Aq | \e \& freecontact \-\-parprof evfold > PF00071_v25_1000.evfold \& \& freecontact \-\-parprof evfold \-i xml \-o bioxsd < \*(Aq/usr/share/doc/freecontact/examples/PF00071_v25_1000.xml\*(Aq > PF00071_v25_1000.evfold.xml \& \& freecontact \-\-parprof psicov < /usr/share/doc/freecontact/examples/demo_1000.aln > demo_1000.psicov .Ve .SH "NOTES" .IX Header "NOTES" For optimal performance, use the Automatically Tuned Linear Algebra Software (\s-1ATLAS\s0) library \fIcompiled on the machine\fR where freecontact is run. .SH "AUTHOR" .IX Header "AUTHOR" László Kaján .SH "SEE ALSO" .IX Header "SEE ALSO" \&\fBjackhmmer\fR\|(1), \fBhhblits\fR\|(1), \fBblastpgp\fR\|(1)