Protein family databases obtain sequences fromone of the large protein sequence databases,most commonly SWISS- PROT with TrEMBL (Bairoch and Apweiler, 2000) but also PIR (Barker et al., 2000). They then apply an algorithm, either manual or automatic, to group the sequences into families. Each family is represented in one or more ways to facilitate both inspection by humans and comparison by computer programs. The most common representation is a multiple alignment of the family’s sequences, either with insertion and deletion (gap) characters or without. Sometimes the multiple alignment is summarized as a pattern or consensus sequence. For comparison of a user’s query sequence with the protein family database, the multiple alignment is commonly converted.
