In Bioinformatics, multiple alignment can be used to study evolutionary relationships between related proteins. Since the changes between gene sequences due to evolution are incremental, we can take homologous genes , i.e. genes with a common evolutionary origin, from a diverse range of organisms and then compare them by aligning identical or similar residues. The comparison of these related genes may then be used to study, which regions of genes have been conserved, and which are sensitive to mutation, over the years. This is very useful in designing experiments to test and modify the function of specific proteins, and to predict the function and structure of proteins, and to identify new members of protein families.
Multiple Sequence Alignment programs and techniques
A common approach for multiple sequence alignment is to progressively align pairs of sequences. First two sequences are selected and are aligned together, and then this alignment is used to align each subsequent sequences.
One of the most popular programs for multiple sequence alignment is known as ClustalW [1]. It is a general purpose multiple alignment program for DNA or proteins. It calculates the best match for the selected sequences, and lines them up so that the similarities and differences can be seen. It also generates a cladogram which can be useful for studying the evolutionary relationships between the set of sequences.