A preliminary work on evolutionary identification of protein variants and new proteins on grids
peer-reviewed · 20th International Conference on Advanced Information Networking and Applications - Volume 1 (AINA’06) · 2006
peer-reviewed · 20th International Conference on Advanced Information Networking and Applications - Volume 1 (AINA’06) · 2006. Jean-Charles Boisson et al. Protein identification is one of the major task of Proteomics researchers. Protein…
| Date | 2006-05-25 |
| Type | peer-reviewed |
| Venue | 20th International Conference on Advanced Information Networking and Applications - Volume 1 (AINA’06) |
| Publisher | IEEE |
| Contribution | algorithm |
| DOI | 10.1109/aina.2006.48 |
| Citations (OpenAlex) | 2 |
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.
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.