A Preliminary Work on Evolutionary Identification of Protein Variants and New Proteins on Grids

postprint · arXiv · 2008

postprint · arXiv · 2008. Jean-Charles Boisson et al. Protein identification is one of the major task of Proteomics researchers. Protein identification could be…
Date 2008-04-08
Type postprint
Venue arXiv
Contribution algorithm
DOI 10.48550/arxiv.0804.1202
Citations (OpenAlex) 0

Abstract

Protein identification is one of the major task of Proteomics researchers. Protein identification could be resumed by searching the best match between an experimental mass spectrum and proteins from a database. Nevertheless this approach can not be used to identify new proteins or protein variants. In this paper an evolutionary approach is proposed to discover new proteins or protein variants thanks a “de novo sequencing” method. This approach has been experimented on a specific grid called Grid5000 with simulated spectra and also real spectra.

Authors

  1. Jean-Charles Boisson · Centre Inria de l’Université de Lille, Institut national de recherche en sciences et technologies du numérique, LIFL / INRIA, Laboratoire d’Informatique Fondamentale de Lille, Université de Lille
  2. Laetitia Jourdan · Centre Inria de l’Université de Lille, Institut national de recherche en sciences et technologies du numérique, LIFL / INRIA, Laboratoire d’Informatique Fondamentale de Lille, Université de Lille
  3. El-Ghazali Talbi · Centre Inria de l’Université de Lille, Institut national de recherche en sciences et technologies du numérique, LIFL / INRIA, Laboratoire d’Informatique Fondamentale de Lille, Université de Lille

Methods and tools

  • Adaptive GA for tandem-MS peptide sequencing: Adaptive genetic algorithm for protein sequencing from tandem MS. Represents peptides as GA individuals, evolves them against the observed spectrum; the adaptive component tunes mutation / crossover rates on the fly.

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