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Bioinformatics is of paramount importance for protein analysis in proteomic and transcriptomic studies. Bioinformatics is used at two steps of proteomic studies : (i) identification of proteins by peptide mass mapping or peptide sequencing and, (ii) analysis of protein sequences to predict their sub-cellular localization and their function. It is also used to sort genes identified by transcriptomic studies in functional classes. In addition, it provides predictions of co-expression networks thus allowing to visualize biological networks. To facilitate interpretation of proteomic and transcriptomic data, ProtAnnDB (Protein Annotation DataBase) collects predictions of sub-cellular localization and of functional domains made by available software on Arabidopsis thaliana, Oryza sativa and Brachypodium distachyon proteins.

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