Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model app

Background: Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include the development of classification systems capable of distinguishing between subfamilies within a structurally and functionally diverse superfamily. This would be helpful in elucidating sequencestructure-function relationships of proteins. Results: Here, we present a method to diagnose sequences into subfamilies by employing hidden Markov models (HMMs) to find windows of residues that are distinct among subfamilies (called signatures). The method starts with a multiple sequence alignment (MSA) of the subfamily. Then, we build a HMM database representing all sliding windows of the MSA of a fixed size. Finally, we construct a HMM histogram of the matches of each sliding window in the entire superfamily. To illustrate the efficacy of the method, we have applied the analysis to find subfamily signatures in two wel...

• Type: Journal
• Year: 2002
• Where: BMCBI
• Authors: Kevin Truong, Mitsuhiko Ikura
• Keywords: BMCBI 2002, Databases, Proteins, Subfamilies