Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison

Background: Detection of common evolutionary origin (homology) is a primary means of inferring protein structure and function. At present, comparison of protein families represented as sequence profiles is arguably the most effective homology detection strategy. However, finding the best way to represent evolutionary information of a protein sequence family in the profile, to compare profiles and to estimate the biological significance of such comparisons, remains an active area of research. Results: Here, we present a new homology detection method based on sequence profile-profile comparison. The method has a number of new features including position-dependent gap penalties and a global score system. Position-dependent gap penalties provide a more biologically relevant way to represent and align protein families as sequence profiles. The global score system enables an analytical solution of the statistical parameters needed to estimate the statistical significance of profile-profile ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Mindaugas Margelevicius, Ceslovas Venclovas
• Keywords: BMCBI 2010, Homology Detection, Position-dependent Gap Penalties, Proteins