Increase in online available bioinformatics tools for protein research creates an important opportunity for scientists to reveal characteristics of the protein of interest by only starting from the predicted or known amino acid sequence without fully depending on experimental approaches. There are many sophisticated tools used for diverse purposes; however, there are not enough reviews covering the tips and tricks in selecting and using the correct tools as the literature mainly state the promotion of the new ones. In this review, with the aim of providing young scientists with no specific experience on protein work a reliable starting point for in silico analysis of the protein of interest, we summarized tools for annotation, identification of motifs and domains, determination isoelectric point, molecular weight, subcellular localization, and post-translational modifications by focusing on the important points to be considered while selecting from online available tools.

In the present study, 47 PMEI type 1 genes and 57 PMEI type 2 genes were identified with bioinformatic analysis. The PMEI genes were localized separately on chromosomes 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21 and 22, but mainly at the level of the scaffold. The biological functions of the PMEI type 1 genes were found to be in the areas of biological regulation, metabolism and cellular functions. Their cellular localization appears to be associated with cell parts. For the PMEI type 2 genes, the biological functions were determined as biological regulation, metabolic and cellular functions. A total of 393 Arabidopsis miRNAs targeting 47 olive PMEI type 1 genes were identified. Two specific miRNAs targeting the OePMEI1-07 gene were found (ath-miR8168 and ath-miR774b-5p). For the PMEI type 2 genes, 269 Arabidopsis miRNAs were found, including 14 specific miRNAs targeting OPMEI2-02, OPMEI2-03, OPMEI2-27, OPMEI2-28, OPMEI2-29, OPMEI2-30, OPMEI2-40 and OPMEI2-54. These results suggest that PMEI genes in olives may not only play a role in cell development, germ cell formation and plant growth, but also play an important role in abiotic and biotic stress conditions in the olive.