Protein Functional Annotation by Homology

Genome sequencing projects have resulted in a rapid accumulation of predicted protein sequences. With experimentally verified information on protein function lagging far behind, computational methods are used for functional annotation of proteins. Here we describe a number of protocols for protein sequence and structure analysis that can be used to infer function of uncharacterized proteins. These protocols rely on publicly available computational resources and tools and can be utilized by anyone with an Internet access.