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| HAL : hal-00678339, version 1 |
| Fiche détaillée |  Récupérer au format |
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| DegenRev: Degeneracy-Based Full Backtranslation Algorithm for Oligopeptide |
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| Mohieddine Missaoui 1, 2David Hill 1 |
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| (05/07/2007) |
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| 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. |
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| 1 : | Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS) |
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CNRS : UMR6158 – Université d'Auvergne - Clermont-Ferrand I – Université Blaise Pascal - Clermont-Ferrand II – Institut Français de Mécanique Avancée |
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| 2 : | Microorganismes : génome et environnement (LMGE) |
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CNRS : UMR6023 – Université Blaise Pascal - Clermont-Ferrand II – Université d'Auvergne - Clermont-Ferrand I |
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| LIMOS |
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| Domaine | : | Informatique/Recherche opérationnelle Informatique/Calcul parallèle, distribué et partagé |
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| Degeneracy – Oligopeptide – Full backtranslation |
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| hal-00678339, version 1 | |
| http://hal.archives-ouvertes.fr/hal-00678339 | |
| oai:hal.archives-ouvertes.fr:hal-00678339 | |
| Contributeur : Secrétariat Limos | |
| Soumis le : Lundi 12 Mars 2012, 15:13:22 | |
| Dernière modification le : Lundi 12 Mars 2012, 16:02:52 | |
