Protein Sequence Databases

Protein sequence databases do not contain just the sequence of the protein itself but also annotation that reflects our knowledge of its function and contributing residues. In this chapter, we will discuss various public protein sequence databases, with a focus on those that are generally applicable. Special attention is paid to issues related to the reliability of both sequence and annotation, as those are fundamental to many questions researchers will ask. Using both well-annotated and scarcely annotated human proteins as examples, it will be shown what information about the targets can be collected from freely available Internet resources and how this information can be used. The results are shown to be summarized in a simple graphical model of the protein’s sequence architecture highlighting its structural and functional modules.