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Pepteam

PepTeam is a tool for biomarker discovery through the analysis of screened repertoires of phage displayed libraries that have been sequenced by NGS. Peptide repertoires are mapped against the proteome of the target organism and functional analysis is performed assuming that small peptides mimic interactions of larger proteins.

Installation

System Requirements

PepTeam is a C++ program developped and intended to be used under a GNU/Linux system

  • G++ >= 4.8.1
  • Boost libraries >= 1.46.1

Obtaining PepTeam

The source code repository for the version currently in deployment inside the CBIB is available at

Installing PepTeam

Grab the version that you are interested in using and use Make. For example, for the version currently in deployment do :

git clone git://github.com/cbib/pepteam
cd PepTeam
make

Usage

Pipeline

PepTeam is implemented as a multi-steps pipeline

  • first preproccess the inputs FASTA files into fastIdx indices files
  • create two pepTree acceleration structures from those two fastIdx preprocessed files
  • map the two pepTree files one against the other
  • extract profile information from the mappings

Example : in order to map a peptide repertoire A.txt, each peptide of size 7, onto a MusMusculus.fa proteome database, with a similarity threshold of 0.25, do the following :

bin/FastIdx -c A.txt
bin/FastIdx -c MusMusculus.fa
bin/PepTree -c A.txt.fastIdx 7
bin/PepTree -c MusMusculus.fa.fastIdx 7
bin/PepteamMap A.txt.fastIdx.pepTree.7 MusMusculus.fa.fastIdx.pepTree.7 0.25
bin/PepteamProfile A.txt.fastIdx.pepTree.7.mapping.0_25 A.txt.fastIdx A.txt.fastIdx.pepTree.7 MusMusculus.fa.fastIdx MusMusculus.fa.fastIdx.pepTree.7

Details

The detailed usage of each program follows

FastIdx

Transform an input multi-fasta file into a .fastIdx index.

Usage: bin/FastIdx -* input-file
   where * is one of:
     c -> create the protein index from input fasta file
     s -> print the number of proteins in the index
     p -> print the index in human 'interpretable' formatPepTree

PepTree

Transform an input .fastIdx index into a serialized .pepTree.x tree structure representing the set of all windows of size x in the input.

Usage: bin/PepTree -c input-FastIdx-file fragments-size
          create the PepTree file from the input FastIdx file
   or: bin/PepTree -% pepTree-file
   where % is one of:
     d -> print the tree depth
     v -> print the tree vector in human 'interpretable' format
     n -> print the tree nodes in human 'interpretable' format
     l -> print the tree leaves in human 'interpretable' format
     p -> print the tree leaf positions in human 'interpretable' format

PepteamMap

Map the first input tree onto the second with a given similarity threshold.

Usage: bin/PepteamMap pepTree-query-file pepTree-subject-file cutoff-homology

PepteamProfile

Construct the profiles for each protein of the proteome database with valid mappings

Usage: bin/PepteamProfile mapping-file query-fastIdx-file query-pepTree-file subject-fastIdx-file subject-pepTree-file

PepteamScoring

Give a score for each protein depending on peptides mapped

Usage: bin/clt_test.py -i peptides.fastIdx.pepTree.k.mapping.h.profiles

  • input : PepteamProfile output file

  • output : 2 files, one in tsv and one in csv showing protein with significant score

###Pepteam annotation

Annotate each protein using Ensembl biomart tools

Usage: pepteamAnnot.pl --input1=database_file --input2=significance.tsv --output=output

  • input : tsv file produced by the previous script clt_test.py. this file contains 3 columns, one for protein ID, one for p-value(>0.05) and finally the Z-score

  • output : a csv annotatted file

here is a example of annotated file:

"Ensembl proteinId" ,"p-value"     ,"Zscore","Ensembl geneID"    ,EntrezgeneId","associated gene name","description", "wikigene description" 
"ENSMUSP00000037233","6.797434e-09","5.6784","ENSMUSG00000039967","30046","Zfp292","zinc finger protein 292 [Source:MGI Symbol;Acc:MGI:1353423]","zinc finger protein 292" 
"ENSMUSP00000095766","7.122627e-09","5.6704","ENSMUSG00000039967","30046","Zfp292","zinc finger protein 292 [Source:MGI Symbol;Acc:MGI:1353423]","zinc finger protein 292"

Licence

Copyright (c) 2013, Thomas Hume (1,2), Hayssam Soueidan (2,3), Benjamin Dartigues (2), and Macha Nikolski (1,2)

(1) LaBRI, Université de Bordeaux, 351 cours de la Libération, 33405 Talence Cedex, France
(2) CBiB, Université de Bordeaux, 146, rue Léo Saignat 33076 Bordeaux
(3) INSERM U1035, Université de Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux

All rights reserved.

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