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PROFISIS

NAME

profisis − protein−protein interaction sites identified from sequence

SYNOPSIS

profisis [ OPTION ]

DESCRIPTION

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 <https://www.rostlab.org/owiki/index.php/How_to_generate_an_HSSP_file_from_alignment#Generating_an_HSSP_profile>.
1. Convert BLAST output to a Single Alignment Format ( SAF ):

 /usr/share/librg−utils−perl/blast2saf.pl 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/copf.pl <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/hssp_filter.pl red=80 <hssp_formatted_file> fileOut=<filtered_hssp_formatted_file>

Output format
See description of −−outformat option.

REFERENCES

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

OPTIONS

Required parameters
−−fastafile

file that contains your sequence in fasta format

−−hsspfile

file with hssp data for sequence in −−fastafile

−−rdbproffile

file with prof output for sequence in −−fastafile

−−outfile

output file

Optional parameters
−−outformat

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.

prval

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

 '1 M 25'
 '2 R 36'
 ...

−−debug
−−nodebug

Default: −−nodebug

−−succinct

Succinct output (print no confidence values).

Parameters controlling post processing − these parameters affect only the top part of the ’pp’ output format
−−gap=int

default=20

−−stretch=int

default=5

−−crd=int

default=7

−−crd−restriction
−−nocrd−restriction

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

EXAMPLES

 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

ENVIRONMENT

PROFISISCONF

Location of configuration file to use, overriding other configuration files

FILES

/usr/share/profisis/profisisrc.default

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

/etc/profisisrc

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

~/.profisisrc

User configuration file overriding values in /etc/profisisrc

$PROFISISCONF

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

AUTHOR

Yanay Ofran and Burkhard Rost

SEE ALSO

prof(1)

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