Searching

Perhaps the simplest kind of bioinformatics experiment that you can perform is to search the public databases for information on a specific gene or protein. With EBI Search, you can search across a large number of public databases simultaneously, without needing to know in advance which database is most relevant to you (Figure 11).

Figure 11 Data types that can be searched using EBI Search. You can explore the EMBL-EBI’s data using an interactive, zoomable version of this map.

Controls

Performing a simple search is not necessarily an experiment and thus doesn’t need a control. However, as soon as you use the results of a search to answer a biological question it becomes an experiment. For example, if you want to find all protein sequences with the keyword ‘globin’, this is a search, not an experiment. But if you want to find which kinase proteins are i) in a particular reaction pathway and ii) are upregulated in a particular disease state, this is an experiment and you should add some controls to check that you are drawing correct conclusions from the results. For example, you could check if your search terms map to other unrelated pathways. You might also check to see if your search terms are correctly attached to the biological entry – can you find the same terms in related entries, for example?

To learn how to use EBI Search to study potential targets, follow the guided example on ZAP70