| Autor: |
Ambroise, Jérôme, Deccache, Yann, Irenge, Leonid, Savov, Encho, Robert, Annie, Gala, Jean-Luc |
| Předmět: |
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| Zdroj: |
Bioinformatics; Dec2014, Vol. 30 Issue 24, p3590-3597, 8p |
| Abstrakt: |
Motivation: Pyrosequencing is a cost-effective DNA sequencing technology that has many applications, including rapid genotyping of a broad spectrum of bacteria. When molecular typing requires to genotype multiple DNA stretches, several pyrosequencing primers could be used simultaneously but this would create overlapping primer-specific signals, which are visually uninterpretable. Accordingly, the objective was to develop a new method for signal processing (AdvISER-M-PYRO) to automatically analyze and interpret multiplex pyrosequencing signals. In parallel, the nucleotide dispensation order was improved by developing the SENATOR (‘SElecting the Nucleotide dispensATion Order’) algorithm.Results: In this proof-of-concept study, quintuplex pyrosequencing was applied on eight bacterial DNA and targeted genetic alterations underlying resistance to β-lactam antibiotics. Using SENATOR-driven dispensation order, all genetic variants (31 of 31; 100%) were correctly identified with AdvISER-M-PYRO. Among nine expected negative results, there was only one false positive that was tagged with an ‘unsafe’ label.Availability and implementation: SENATOR and AdvISER-M-PYRO are implemented in the AdvISER-M-PYRO R package (http://sites.uclouvain.be/md-ctma/index.php/softwares) and can be used to improve the dispensation order and to analyze multiplex pyrosequencing signals generated in a broad range of typing applications.Contact: jerome.ambroise@uclouvain.be [ABSTRACT FROM AUTHOR] |
| Databáze: |
Complementary Index |
| Externí odkaz: |
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