VAMA: A Versatile Web-Based Tool for Variability Analysis in Multiply-Aligned Amino Acid Sequences: VAMA: Variability Analysis of Multiple Alignments

Quantifying residue variability at each column in a multiple sequence alignment of amino acids helps in indicating their similarities, and is useful to highlight information about the significances of each position from the perspective of their structure, function, and evolution. It is becoming increasingly clear that the groups of amino acids that allow conserved replacement vary with the position of the residue in the protein. Most multiple alignment algorithms cater to general users and hence do not address this specific feature. A tool for scoring variability in multiply-aligned amino acid sequences, that allows different conservation groups, is highly desirable. VAMA (Variability Analysis of Multiple Alignments) is a simple yet versatile program that calculates and plots residue variability in a given set of aligned sequences based on known conservation groups specific for different functionally important regions of a protein, and also allows user-defined groups for new discoveries. VAMA is available at http://203.200.217.184/VAMA/Overview.html.