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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).
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The database was analysed using SPSS Version 19.
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).
Data were collected into a dedicated Excel database, and were analysed using EpiData v.2.2.1.171 software (EpiData Association, Odense, Denmark).
Results were entered into Microsoft Access 2007 database and were analysed using the 'R' environment for statistical computing [ 31]. 390 pigs were sampled from 6 districts in the Lake Kyoga region.
To identify transcription factors (TFs), the MSU locus IDs of all selected DEGs were analysed using Database of Rice Transcription Factors (DRTF), GRASSIUS and RiceFREND (Gao et al. 2006; Yilmaz et al. 2009; Sato et al. 2013).
The lists of differentially expressed genes were analysed using the Database for Annotation, Visualisation and Integrated Discovery (DAVID) Bioinformatics Resources (Huang et al. [2008]) and are discussed in relation to gross and microscopic changes induced by ethephon application.
The cDNA sequences were analysed using Genbank database (http://www.ncbi.nlm.nih.gov).nih.gov
Class 1 and 2 integrons were analysed using INTEGRAL database (http://integrall.bio.ua.pt/?).bio.ua.pt/
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