A Sequence Alignment Algorithm and Tools for Molecular Replacement

Abstract

This paper describes a new genetic alignment algorithm and software tool for sequences that can be used for determination of deletions and substitutions. Sequence alignment is one of the most active ongoing research problems in the field of computational molecular biology. Sequence alignment is important because it allows scientists to analyze protein strands (such as DNA and RNA) and determine where there are overlaps. This overlaps can show commonalities in evolution and they also allow scientists to better prepare vaccines against viruses, which are made of protein strands. The algorithm provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or other considerations. The algorithm does not use similarity tables and it performs aspects of both global and local alignment. It is also compared with other sequence alignment algorithms.