Pfam: A Domain-Centric Method for Analyzing Proteins and Proteomes

The constant deluge of genome sequencing data means that annotating, classifying, and comparing proteins or proteomes can seam like an endless task. Furthermore, discovering and accessing such data is fundamental to biologists. There are, however, databases that perform these tasks. Pfam, a protein families database, is one such database. In this chapter, the use of the web interface to Pfam and the resources provided (annotation, sequence alignments, phylogenetic trees, profile hidden Markov models [HMMs]) are described. The exploitation of tools for searching sequences against the library of Pfam HMMs, searching for domain combinations, searching by taxonomy, browsing proteomes, and comparing proteomes are outlined in detail.