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Sipros3.1

Sipros is a database searching program for shotgun proteomics. It can perform accurate general-purpose protein identification, broad-range post-translational modification searches, and stable isotope probing. Hybrid MPI/OpenMP parallelism of the new Sipros architecture allows its computation to be scalable from desktops to supercomputers. Sipros was integrated with ProRata for label-free quantification, metabolic labeling quantification, and isobaric chemical labeling quantification (TMT/iTRAQ).

Key applications:

  1. Regular database searching

  2. Stable isotope probing

  3. Identification of post-translational modifications

  4. Identification of amino acid mutations.

Unique features:

  1. Scalable to high-performance computing

  2. Full integration with ProRata for quantification

Installation

MPI version

  1. change the compiler path in two files Sipros3.1/ReleaseMPI/makefile and Sipros3.1/ReleaseMPI/src/subdir.mk.

  2. In Sipros3.1/ReleaseMPI/makefile, edit line 8.

  3. In Sipros3.1/ReleaseMPI/src/subdir.mk, edit line 5.

  4. type cd Sipros3.1/ReleaseMPI/ and then type make.

  5. SiprosMPI will be generated at Sipros3.1/ReleaseMPI/.

OpenMP version

  1. type cd Sipros3.1/ReleaseOpenMP/ and then type make.

  2. Sipros_OpenMP will be generate at Sipros3.1/ReleaseOpenMP/.

Usage

Database Search

  1. Create configure file Please refer to "Configure File Setting" for technical details. An example is available at http://code.google.com/p/sipros/source/browse/trunk/Sipros3.0/Sipros-src/SiprosConfigRegular.cfg

  2. FT1 and FT2 files Please refer to http://code.google.com/p/raxport/ for generating FT1 and FT2 files

  3. Pre-processing The current version of scripts has been tested using Python 2.7.2, so if you are using different versions of Python (2.6.X or 3.X), you are encouraged to try with Python 2.7.2. If you want to use reverseseq.py, Biopython is required. cd Sipros3.1/scripts

  4. Generate reverse sequence python reverseseq.py -i original_database_file -o output_database_file The step will generate a new database file with reverse sequences.

  5. Run Sipros The easiest way for running Sipros is

./SiprosMPI -c configurefilename -w workingdirectory

or

./Sipros_OpenMP -c configurefilename -w workingdirectory

Sipros will use all .FT2 files in the working directory. Results (.sip files) will be saved on working directory by default. You can specify output directory by specifying -o. If you just want to specify one FT2 file, you can use -f like,

./SiprosMPI -c configurefilename -f FT2filename

or

./Sipros_OpenMP -c configurefilename -f FT2filename

If you want to slice screen output, please add -s. In SiprosMPI, you are allowing to specify -g like,

./SiprosMPI -g configurefiledirectory -w workingdirectory, if you have many configure files.

Please note that you can get help information by flag -h.

Post-processing

The current version of scripts has been tested using Python 2.7.2, so if you are using different versions of Python (2.6.X or 3.X), you are encouraged to try with Python 2.7.2.

cd Sipros3.1/scripts

Peptide filtering

python sipros_peptides_filtering.py -c configurefile -w workingdirectory All sip files, output files of Sipros, should be in the working directory. The step will generate related psm.txt and pep.txt

Peptide assembling

python sipros_peptides_assembling.py -c configurefile -w workingdirectory The psm.txt and pep.txt files generated by the filtering step will be used in this step. And the step will generate pro.txt, pro2pep.txt, and pro2psm.txt files

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