GenoSuite Files

GenoSuite
Version:2.0.1
Created and maintained by : Dhirendra Kumar
for Quesries and feed back mail to
dhirendra@igib.in
ddash@igib.in
##################################################################################################################
PPT.exe

Description:
This program performs proteogenomic searches of proteomic data against a genome sequence and list genome search specific peptides. 

Usase: 
PPT.exe Prokaryotic Proteogenomic tool 

Dependencies:
1-OMSSA and/or X!Tandem and/or Inspect and/or MassWiz
OMSSA can be downloaded at 
http://pubchem.ncbi.nlm.nih.gov/omssa/win32.htm
X!Tandem can be downloaded at
ftp://ftp.thegpm.org/projects/tandem/source/
Inspect can be downloaded at
http://proteomics.ucsd.edu/
MassWiz executable is available with standard distributions of the PPT.
2-formatdb.exe(Blast executables).
ftp://ftp.ncbi.nih.gov/blast/executables/release/2.2.18/
or
http://code.google.com/p/mass-spec-gui/downloads/detail?name=formatdb.exe&can=2&q=


INPUT file format
###########################
#comments
##########################
-g=./DATABASE/genome.fasta;	#path for filecontaining genome sequence in FASTA format
-p=./DATABASE/proteome.fasta;	#path for file containing known protein sequences in FASTA format
-O=./OMSSA;			#OMSSA directory path. Program tries to find omssacl.exe in this directory.
-T=./Tandem;			#TANDEM directory path. Program tries to find /bin/Tandem.exe in this directory.
-I=./INSPECT;			#INSPECT directory path. Program tries to find Inspect.exe in this directory.
-M=./MassWiz;			#MassWiz directory path. Program tries to find MassWiz_parallel.exe in this directory.
-s=./INPUT;			#Directory path containing mgf files
-r=params.txt;			#parameter file(Please see default_params.txt)
-f=./DATABASE/;			#formatdb.exe directory path. program tries to find formatdb.exe in this directory.
-d=1;				#Decoy type. 1 for Separate decoy. 0 for concatenated decoy. Needed while creating the database.

-b=./DATABASE/NC_000962.gbk;	#Genebank formatted file
##########################
#comments: Please avoid spaces and special charecters in the file name or path
#########################

Parameter file format
##########################
#Comments
##########################
Enzyme=0;	#Protease enzyme ID.0 for trypsin. For enzyme ids please refer ./CONFIG/enzyme_list.txt
MC=1;		#Missed Clevages
PreTol=6;	#Precursor matching tolerance
PreUnit=ppm;	#Unit for precursor tolerance. Available options: ppm or Da.
ProTol=0.8;	#Product ion matching tolerance.
ProUnit=Da;	#Unit for product ion tolerance.Available options:ppm or Da.Omssa supports only Da for product tolerance.
FixedMod=3;	#Fixed modification ID/IDs. Please refer ./CONFIG/mod_list.txt for modification ids. 
VarMod=1;	#variable modification ID/IDs. Please refer ./CONFIG/mod_list.txt for modification ids. 
SpectraFile=;	#Spectra file path. Leave blank as file names will be read from the dierctory path provided automatically.
Database=;	#Database file. Leave blank as database is created by translating the genome file.
Decoy_Database=;#Decoy database file. Leave blank as decoy database is created by reversing the translated genome file.
FDR_Value=1;	#FDR cutoff value. Separate FDR is calculated.
FDR_Type=1;	#FDR Type. 1 for Separate target decoy Search. 0 for Concatenated target decoy search. Default 1.
###########################
#Comments
###########################

OUTPUTs:
Program outputs various files in a separate folder created for each search run. These folders are named after the search start date and time. All output folders are created in OUTPUT directory in the current path.
For a search project a Result_Summary folder holds the final processed results.

Summary Results contain.... 

1) Novel proteins identified with 2 or more peptides or single peptide hits with minimum 5 PSMs.
2) A list of gene model changes suggested by the identified upstream peptides.
3) A list of known protein identified with 2 or more peptides or in case of single peptide hit should be identified with at least 5 significant hits.
4) A consolidated GFF of unique peptides.

Additional files for each of the MGF file searched are
1) FDR(Combined FDRScore) corrected PSMs after integration of results from multiple searched algorithms.
2) A list of proteins identified.
3) Novel proteins identified.
4) Gene model changes identified.
5) Proteins identified with single peptides and less than 5 PSMs.
6) GFF of significant  novel peptides.



##################################################################################################################


Orf_mapper.exe


Description:
This program maps orfs to the novel peptides and categorises peptides in Novel proteins or changes in existing gene models on the basis of CDS information provided in Genbank file. 

Usase: 
Orf_mapper.exe -f genbank_filename -F ORFprediction_file_name -y GFF -P PeptideGFF -e 1 -g P

-f genbank filename having the CDS co-ordinates.
-F ORF prediction GFF file
-y Prediction file format. Allowed values GENEMARK/GFF.
-P Peptide GFF filename
-e flag for html report genartion. Allowed values are 0/1. Default 0.
-g group of the organism. Allowed values are P/E. P for prokaryote. E for Eukaryote.


OUTPUT:
Program outputs an HTML with hyperlinks of images showing genomic context of the novel peptide. In addition to HTML a text file listing suspected N-terminal changes (Changes in translation start site) to the existing gene models and in another text file lists novel proteins(Where no gene model is found in the genbank file).
##################################################################################################################


PSM_plotter.exe

Description:
This programs plots the peptide spectral matches. Reads XML created after search performed by PPT.exe.
Programs outputs an HTML file with hyperlinks of images for each PSM identified.

Usase: 
PSM_plotter.exe -X PSM.xml

OUTPUT:
Program outputs an HTML with hyperlinks of peptide spectral match images. 

#################################################################################################################