The JRC GMO-Matrix is an application that takes advantage of the GMO sequence information found in the Central Core DNA Sequence Information System (CCSIS), which are received from companies as part of their legal obligations or extracted from nucleotide / patent sequences databases, as well as the primers and probes sequences of the existing detection methods compiled in the GMOMETHODS database to perform in silico simulations of PCR amplification and, when applicable, probe binding using bioinformatics tools, such as re-PCR and matcher.
JRC GMO-Matrix application relies on a relational database that contains pre-computed values corresponding to the extent of matching between the methods primers and probe and each GMO sequence. Those pre-calculated values represent the results of in silico simulations of the detection of each GMO by each PCR-based detection method and form the core data used by the application for its different case uses. The pre-calculations are made using "re-PCR" (Rotmistrovsky et al, 2004) for detecting potential amplicons and "matcher" from the EMBOSS package (Rice et al. 2000) to test probe annealing when the method contains one
The current version of the JRC GMO-Matrix application contains a set interfaces available to the user, which is expected to grow based on the feedback that will be received.
These are:
This interface can be used for building two-dimensional matrices (chosen GMO events vs chosen GMO methods) in order to visualise the universal coverage of the detection methods and identify potential gaps.
This interface allows identification of potential GMO(s) present in the sample based on a set of positive and negative detection method experimental results
A ready-to-use, multi-target screening tool known as the pre-spotted plate (PSP) has recently been developed. This PSP allows testing for the presence of multiple GMO-targets in a single PCR experiment and is therefore expected to offer important advantages in terms of cost and time. This interface provides a web-based tool to facilitate the interpretation of results.
For more information, see:
"JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies."
BMC Bioinformatics. 2014 Dec 30;15(1):6592. link
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© European Union, 2014
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