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.\" ========================================================================
.\"
.IX Title "PROFISIS 1"
.TH PROFISIS 1 "2018-10-14" "1.0.11" "User Commands"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
profisis \- protein\-protein interaction sites identified from sequence
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
profisis [\s-1OPTION\s0]
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
profisis (\s-1ISIS\s0) is a machine learning-based method that identifies interacting residues from sequence alone. Although the method is developed using transient protein-protein interfaces from complexes of experimentally known 3D structures, it never explicitly uses 3D infor\- mation. Instead, we combine predicted structural features with evolutionary information. The strongest predictions of the method reached over 90% accuracy in a cross-validation experiment. Our results suggest that despite the significant diversity in the nature of protein-protein interactions, they all share common basic principles and that these principles are identifiable from sequence alone.
.SS "Conversion of PSI-BLAST alignment to \s-1HSSP\s0 format"
.IX Subsection "Conversion of PSI-BLAST alignment to HSSP format"
The most up-to-date procedure can be found at <https://www.rostlab.org/owiki/index.php/How_to_generate_an_HSSP_file_from_alignment#Generating_an_HSSP_profile>.
.IP "1. Convert \s-1BLAST\s0 output to a Single Alignment Format (\s-1SAF\s0):" 4
.IX Item "1. Convert BLAST output to a Single Alignment Format (SAF):"
.Vb 2
\& /usr/share/librg\-utils\-perl/blast2saf.pl fasta=<query_fasta_file> maxAli=3000 eSaf=1 \e
\&  saf=<saf_formatted_file> <blast_output>
.Ve
.IP "2. Convert \s-1SAF\s0 format to \s-1HSSP:\s0" 4
.IX Item "2. Convert SAF format to HSSP:"
.Vb 2
\& /usr/share/librg\-utils\-perl/copf.pl <saf_formatted_file> formatIn=saf formatOut=hssp \e
\&  fileOut=<hssp_formatted_file> exeConvertSeq=convert_seq
.Ve
.IP "3. Filter results to 80% redundancy:" 4
.IX Item "3. Filter results to 80% redundancy:"
.Vb 1
\& /usr/share/librg\-utils\-perl/hssp_filter.pl red=80 <hssp_formatted_file> fileOut=<filtered_hssp_formatted_file>
.Ve
.SS "Output format"
.IX Subsection "Output format"
See description of \fB\-\-outformat\fR option.
.SH "REFERENCES"
.IX Header "REFERENCES"
.IP "Ofran, Y. and Rost, B. (2007). \s-1ISIS:\s0 interaction sites identified from sequence.  Bioinformatics, 23(2), e13\-6." 4
.IX Item "Ofran, Y. and Rost, B. (2007). ISIS: interaction sites identified from sequence. Bioinformatics, 23(2), e13-6."
.SH "OPTIONS"
.IX Header "OPTIONS"
Required parameters
.IP "\-\-fastafile" 4
.IX Item "--fastafile"
file that contains your sequence in fasta format
.IP "\-\-hsspfile" 4
.IX Item "--hsspfile"
file with hssp data for sequence in \-\-fastafile
.IP "\-\-rdbproffile" 4
.IX Item "--rdbproffile"
file with prof output for sequence in \-\-fastafile
.IP "\-\-outfile" 4
.IX Item "--outfile"
output file
.PP
Optional parameters
.IP "\-\-outformat" 4
.IX Item "--outformat"
output format [pp|prval], default=pp
.RS 4
.IP "pp" 4
.IX Item "pp"
PredictProtein format:
.Sp
.Vb 1
\& Output ::= Header_Line Binary_Out Raw_Out
\&
\& Header_Line ::= \*(Aq>\*(Aq Header_String \*(Aq\en\*(Aq
\&
\& Binary_Out ::= ( Horiz_Sequence \*(Aq\en\*(Aq Bin_Pred \*(Aq\en\en\*(Aq )+
\&
\& Horiz_Sequence ::= Amino_Acid_One_Letter_Code{,40}
\&
\& Bin_Pred ::= [P\-]{,40}
.Ve
.Sp
\&'P' marks binding residue.
.Sp
.Vb 1
\& Raw_Out ::= ( Amino_Acid_Number \*(Aq \*(Aq Amino_Acid_One_Letter_Code \*(Aq \*(Aq Prediction_Score \*(Aq\en\*(Aq )+
\&
\& Prediction_Score ::= Integer_Value
.Ve
.Sp
See example outputs in \fI/usr/share/doc/profisis/examples\fR.
.IP "prval" 4
.IX Item "prval"
( 'resn resi predicted_value' )+, e.g.
.Sp
.Vb 3
\& \*(Aq1 M 25\*(Aq
\& \*(Aq2 R 36\*(Aq
\& ...
.Ve
.RE
.RS 4
.RE
.IP "\-\-debug" 4
.IX Item "--debug"
.PD 0
.IP "\-\-nodebug" 4
.IX Item "--nodebug"
.PD
Default: \-\-nodebug
.IP "\-\-succinct" 4
.IX Item "--succinct"
Succinct output (print no confidence values).
.PP
Parameters controlling post processing \- these parameters affect only the top part of the 'pp' output format
.IP "\-\-gap=int" 4
.IX Item "--gap=int"
default=20
.IP "\-\-stretch=int" 4
.IX Item "--stretch=int"
default=5
.IP "\-\-crd=int" 4
.IX Item "--crd=int"
default=7
.IP "\-\-crd\-restriction" 4
.IX Item "--crd-restriction"
.PD 0
.IP "\-\-nocrd\-restriction" 4
.IX Item "--nocrd-restriction"
.PD
Default: \-\-crd\-restriction. Use original ($crd = undef) code (\-\-crd\-restriction) or use new ($cr) code (\-\-nocrd\-restriction).
.SH "EXAMPLES"
.IX Header "EXAMPLES"
.Vb 1
\& profisis \-\-fastafile /usr/share/doc/profisis/examples/3A1P_A.fasta \-\-hsspfile /usr/share/doc/profisis/examples/3A1P_A.hssp \-\-rdbproffile /usr/share/doc/profisis/examples/3A1P_A.rdbProf \-\-outfile /tmp/3A1P_A.profisis
.Ve
.SH "ENVIRONMENT"
.IX Header "ENVIRONMENT"
.IP "\s-1PROFISISCONF\s0" 4
.IX Item "PROFISISCONF"
Location of configuration file to use, overriding other configuration files
.SH "FILES"
.IX Header "FILES"
.IP "\fI/usr/share/profisis/profisisrc.default\fR" 4
.IX Item "/usr/share/profisis/profisisrc.default"
Default configuration file. See this file for a description of the parameters.
.IP "\fI/etc/profisisrc\fR" 4
.IX Item "/etc/profisisrc"
System configuration file overriding values in \fI/usr/share/profisis/profisisrc.default\fR
.IP "\fI~/.profisisrc\fR" 4
.IX Item "~/.profisisrc"
User configuration file overriding values in \fI/etc/profisisrc\fR
.IP "\fI\f(CI$PROFISISCONF\fI\fR" 4
.IX Item "$PROFISISCONF"
If this environment variable is set \fI~/.profisisrc\fR is disregarded and the value of the variable is read for configuration options overriding \fI/etc/profisisrc\fR
.SH "AUTHOR"
.IX Header "AUTHOR"
Yanay Ofran and Burkhard Rost
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fIprof\fR\|(1)