DegenRev: Degeneracy-Based Full Backtranslation Algorithm for Oligopeptide

Mohieddine Missaoui (1) , David R.C. Hill (2) , Pierre Peyret (3)

1 LIMOS - Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes
2 LIMOS - Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes
3 LMGE - Laboratoire Microorganismes : Génome et Environnement

In order to design microarray oligonucleotides, in the context of new metabolic pathways discovery, it appears that a full backtranslation of oligopeptides is a promising approach. Protein to DNA reverse translation is a time-consuming task that can provide unreasonable quantities of data. This is why most current applications use genetic degenerated code or data mining-based techniques to select the best reverse translation of a short protein sequence called oligopeptide. When the purpose is only to design short oligos it is particularly interesting to have the complete sequences to solve the design problems of enzyme specific oligos for microarrays. In this paper, we revisit existing bioinformatics applications, which bring reverse translation solutions, and we present a new algorithm based on input oligopeptide degeneracy able to efficiently compute a full reverse translation. We propose an implementation with the C programming language and we show its performance statistics on simulated and real biological datasets.

Mots clés: Degeneracy; Oligopeptide; Full backtranslation

Domaines: Recherche opérationnelle [math.OC]; Calcul parallèle, distribué et partagé [cs.DC]

Mohieddine Missaoui, David R.C. Hill, Pierre Peyret. DegenRev: Degeneracy-Based Full Backtranslation Algorithm for Oligopeptide. 2007. ⟨hal-00678339⟩