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
The source code repository for the version currently in deployment inside the CBIB should be available at
The source code repository for the current developmental version is available at
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
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
The detailed usage of each program follows
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
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
Map the first input tree onto the second with a given similarity threshold.
Usage: bin/PepteamMap pepTree-query-file pepTree-subject-file cutoff-homology
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
Copyright (c) 2013, Thomas Hume (1)
(1) LaBRI, Universite Bordeaux 1, 351 cours de la Liberation, 33405 Talence Cedex, France
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