MSblender

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MSblender is a statistical tool for merging database search results from multiple database search engines for peptide identification based on a multivariate modelling approach.

We will present this work at RECOMB-CP 2011 in March, 2011.

Contents

Authors

  • Hyungwon Choi (hwchoi at umich dot edu)
  • [User:Taejoon Taejoon Kwon] (taejoon dot kwon at mail dot utexas dot edu)

Prerequisites

We tested our codes at Mac OSX (10.5 Leopard) and Ubuntu Linux (10.04 and later). We don't support MS Windows platform yet.

To run MSblender, you should install the following programs/packages on the machine.

  • python (2.5 or later)
  • gcc (we used version 4.4.3, but we believe that our ANSI-C based codes are not dependent on specific version of gcc).
  • GNU Scientific Library (version 1.13 or later)
    • If you use ubuntu (or debian) linux, install 'gsl-bin' and 'libgsl0-*' packages.
  • (Optional) [matplotlib (python graph library). Only required for 'pre/plot-his_list.py' script.

Installation

  • Download source code from GitHub. Alternatively, you can download it from http://www.marcottelab.org/users/MSblender/src/MSblender-current.tgz .
  • Enter to 'c/' directory, and execute './compile' script. You should have GNU Scientific Library before running this script. It will generate 'msblender' and 'msblender.h.gch' files at the same directory.
  • That's it. Now you are ready to run MSblender.

How to use

Coming soon..

Citation

  • T. Kwon*, H. Choi*, C. Vogel, A.I. Nesvizhskii, and E.M. Marcotte, MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines. Submitted.

See also