Provided by: profisis_1.0.11-5_all bug


       profisis - protein-protein interaction sites identified from sequence


       profisis [OPTION]


       profisis (ISIS) 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.

   Conversion of PSI-BLAST alignment to HSSP format
       The most up-to-date procedure can be found at

       1. Convert BLAST output to a Single Alignment Format (SAF):
            /usr/share/librg-utils-perl/ fasta=<query_fasta_file> maxAli=3000 eSaf=1 \
             saf=<saf_formatted_file> <blast_output>

       2. Convert SAF format to HSSP:
            /usr/share/librg-utils-perl/ <saf_formatted_file> formatIn=saf formatOut=hssp \
             fileOut=<hssp_formatted_file> exeConvertSeq=convert_seq

       3. Filter results to 80% redundancy:
            /usr/share/librg-utils-perl/ red=80 <hssp_formatted_file> fileOut=<filtered_hssp_formatted_file>

   Output format
       See description of --outformat option.


       Ofran, Y. and Rost, B. (2007). ISIS: interaction sites identified from sequence.
       Bioinformatics, 23(2), e13-6.


       Required parameters

           file that contains your sequence in fasta format

           file with hssp data for sequence in --fastafile

           file with prof output for sequence in --fastafile

           output file

       Optional parameters

           output format [pp|prval], default=pp

           pp  PredictProtein format:

                Output ::= Header_Line Binary_Out Raw_Out

                Header_Line ::= '>' Header_String '\n'

                Binary_Out ::= ( Horiz_Sequence '\n' Bin_Pred '\n\n' )+

                Horiz_Sequence ::= Amino_Acid_One_Letter_Code{,40}

                Bin_Pred ::= [P-]{,40}

               'P' marks binding residue.

                Raw_Out ::= ( Amino_Acid_Number ' ' Amino_Acid_One_Letter_Code ' ' Prediction_Score '\n' )+

                Prediction_Score ::= Integer_Value

               See example outputs in /usr/share/doc/profisis/examples.

               ( 'resn resi predicted_value' )+, e.g.

                '1 M 25'
                '2 R 36'

           Default: --nodebug

           Succinct output (print no confidence values).

       Parameters controlling post processing - these parameters affect only the top part of the
       'pp' output format




           Default: --crd-restriction. Use original ($crd = undef) code (--crd-restriction) or
           use new ($cr) code (--nocrd-restriction).


        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


           Location of configuration file to use, overriding other configuration files


           Default configuration file. See this file for a description of the parameters.

           System configuration file overriding values in /usr/share/profisis/profisisrc.default

           User configuration file overriding values in /etc/profisisrc

           If this environment variable is set ~/.profisisrc is disregarded and the value of the
           variable is read for configuration options overriding /etc/profisisrc


       Yanay Ofran and Burkhard Rost