Journal of Proteomics & Bioinformatics
Open Access

Department of Applied Sciences, Abdelmalek Essaadi University, Tangier, Morocco

Publications

• Research Article   
  A Protein Signatures-Based Decoy Framework for Improved Protein Identification in Target-Decoy Search Approach
  Author(s): Taoufik Bensellak* and Ahmed Moussa
  
  The primary objective of the target-decoy strategy is to estimate the False Discovery Rate (FDR) for reported peptide or protein matches during a protein database search. Various strategies, such as decoy database generation methods and search engine combinations, have been explored. Earlier research investigated the influence of decoy construction models and showed stochastic/statistical methods to be more promising and accurate than basic sequence reversal or shuffling methods. In this paper, we propose a novel decoy creation framework based on proteins’ significant biological signatures, patterns, and profiles, using stochastic models such as Markov. As part of the proposed approach’s flexibility, decoy sequence generation can be adapted to digestion sites and be peptide-based or protein-based. For comparison and benchmark purposes, we investigated a.. View More»
  DOI: 10.35248/0974-276X.24.17.667

  Abstract HTML PDF