DegenRev: Degeneracy-Based Full Backtranslation Algorithm for Oligopeptide - Archive ouverte HAL Access content directly
Reports Year : 2007

DegenRev: Degeneracy-Based Full Backtranslation Algorithm for Oligopeptide

Abstract

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.
Fichier principal
Vignette du fichier
RR-07-10b.pdf (205.01 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

hal-00678339 , version 1 (12-03-2012)

Identifiers

  • HAL Id : hal-00678339 , version 1

Cite

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

Share

Gmail Facebook X LinkedIn More