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, to predict the function and structure of proteins, and to identify new members of protein families.
The production of a protein sequence alignment is a necessary step for the study of the phylogeny of a protein family and for protein ___domain discovery. Some methods of prediction of protein features work better with the protein sequence and its alignment to other sequences, than with the protein sequence alone.
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.
There are many computer programs to produce protein alignments starting with a collection of unaligned sequences (ClustalW, T-Coffee) and to represent graphically those alignments (ClustalW, Belvu).
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