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.
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>
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)