In the last years post-transcriptional regulation (PTR) of gene expression has been increasingly recognized to be a powerful and general determinant of the quantitative changes in proteomes, and therefore a driving force for cell phenotypes. By means of networks of trans-factors on one hand, and cis-elements found primarily in untranslated regions (UTRs) of mRNA on the other hand, mRNA availability to translation and translation rates are tightly controlled and can be rapidly tuned according to the changing state of the cell. A number of dedicated resources and tools, including databases and predictive algorithms, have been proposed as bioinformatics aids for the study of this fundamental layer of gene expression regulation. Their use, however, is rendered difficult by heterogeneity and fragmentation. This review aims to locate these resources in their proper space, classifying them according to their goals, limitations and integration capabilities and, in the end, to provide the user with an initial toolbox for the bioinformatic analysis of post-transcriptional regulation of gene expression. The accompanying website, available at www.ptrguide.org, lists all resources, provides summary and features for each one and will be regularly updated in the future.