Entropy calculator: getting the best from your multiple protein alignments.

Amino acid sequence alignment is an extremely useful tool in protein family analysis. Most family characteristics, such as the localization of functional residues, structural constraints and evolutionary relationships may be retrieved through the observation of the conservation pattern highlighted by the alignments. A quantitative score for the conservation in the alignment allows different stages of an alignment to be compared and consequently the alignment information to be efficiently exploited. Many scoring methods have been proposed during the last three decades. Claude Shannon's theory of communication (1948) paved the way for a consistent scoring of protein alignments by considering the residue (or symbol) frequency. A number of modifications have been proposed since that time, but the core statistical approach is still considered one of the best. By combining many database managing tools for treatment of protein sequences, a ClustalW software integration, a flexible symbols treatment and gap normalization functions, Entropy Calculator software has been developed. This new tool provides a global and optimal approach to multiple sequence alignment scoring by offering an easy graphic interface and a series of modification options that help in interpreting alignments and allow conservation pattern inferences to be performed.