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MULTIPLE SEQUENCE ALIGNMENT (MSA)

Figure 1. Multiple Sequence Alignment of PI 3-kinase Class III. This figure shows the protein sequences and the conserved domains of Arabidopsis thaliana (arabidopsis), Drosophila melanogaster (fruit fly), Homo sapiens (human), Mus musculus (mouse) and Saccharomyces cerevisiae (yeast). This also shows the similarities between the sequences.

A Multiple Sequence Alignment (MSA) is a way to compare protein, RNA and DNA sequences across different species. MSA is often used with an assumption that  the input set of query sequences have an evolutionary relationship by which the species have a lineage and are descended from a common ancestor. From the MSA result, sequence homology can be obtained and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. The alignment result allows users to see a very clear picture in the comparison of different protein, RNA and DNA across different species that especially good at showing mutation events such as point mutations, and insertion or deletion mutations that would appear as hyphens in the alignment result. By running MSA, scientists can look at the conserved regions or domains of different proteins, for example, the catalytic region for PI3-kinase Class III. Therefore, more details can be obtain, e.g. the regulatory region of a protein. The following diagram is an annotated edit of a MSA which was generated by Clustal Omega.

 

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