ArticleBioinformatics (Oxford, England)2013
AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- UGM: a more stable procedure for large-scale multiple testing problems, new solutions to identify oncogene.Theoretical biology & medical modelling · 2019Review
- Using a constraint-based regression method for relative quantification of somatic mutations in pyrosequencing signals: a case for NRAS analysis.Algorithms for molecular biology : AMB · 2016Article
- A qPCR and multiplex pyrosequencing assay combined with automated data processing for rapid and unambiguous detection of ESBL-producers Enterobacteriaceae.AMB Express · 2015Article
- Multiplex pyrosequencing assay using AdvISER-MH-PYRO algorithm: a case for rapid and cost-effective genotyping analysis of prostate cancer risk-associated SNPs.BMC medical genetics · 2015Article
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Authors and funding
8 authors.
Funding
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Abstract
motivationConverting a pyrosequencing signal into a nucleotide sequence appears highly challenging when signal intensities are low (unitary peak heights ) or when complex signals are produced by several target amplicons. In these cases, the pyrosequencing software fails to provide correct nucleotide sequences. Accordingly, the objective was to develop the AdvISER-PYRO algorithm, performing an automated, fast and reliable analysis of pyrosequencing signals that circumvents those limitations.
resultsIn the current mycobacterial amplicon genotyping application, AdvISER-PYRO performed much better than the pyrosequencing software in the following two situations: when converting Single Amplicon Sample (SAS) signals into a correct single sequence (97.2% versus 56.5%), and when translating Multiple Amplicon Sample (MAS) signals into the correct sequence pair (74.5%). AVAILABILITY: AdvISER-PYRO is implemented in an R package (http://sites.uclouvain.be/md-ctma/index.php/softwares) and can be used in broad range of clinical applications including multiplex pyrosequencing and oncogene re-sequencing in heterogeneous tumor cell samples.
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