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The database was analysed using SPSS Version 19.
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All the cases in the database were analysed using the South Asian Name and Group Recognition Algorithm SANGRAA).
To obtain a final annotation table, the annotations from each database were analysed using the BLAST scoring system [ 62] to obtain the best annotation for each transcript.
In addition, this tool has been used to find crop-specific and new traits, and as a test case, 150 traits of the IMIS database were analysed using the subset maize trait ontology (CO_322) and TO; 74 traits were matched to those of maize trait ontology and 35 to those of TO (Fig. 2).
The 7,353 protein sequences from the global assembly that exhibit homology in the protein databases were analysed using a new integrative functional annotation pipeline (Gagnière et al., manuscript in preparation).
The database of promoters was analysed using MEME to identify conserved motifs.
The DEG gene list (of 5345 genes) was analysed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) for pathway analysis.
The quantitative validity of the DESDE-LTC instrument was analysed using a database comprising 1339 services (BSICs), assessed by the core group.
The KEGG pathway proposed on the gene set of M. neglectum by GenDBE was analysed using PRIAM (database profile of March 2013) [ 34, 74].
This was analysed using the KEGG database [ 44].
The functional significance of differentially expressed genes was analysed using the 'Database for Annotation Visualization and Integrated Discovery' (DAVID) (http://david.abcc.ncifcrf.gov).abcc.ncifcrf.gov
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