Establishing a framework for comparative analysis of genome sequences

This paper describes a framework and a high level language tool for comparative analysis of genome sequence alignment. The framework integrates the information derived from multiple sequence alignment and phylogeny to derive new properties about homologous sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment, and to derive mutation related information from a phylogenetic tree by superimposing parsimony. The framework has been applied to derive constrained columns which exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog tool based on the the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns