What is a Multiple Sequence Alignment?

 

A Multiple Sequence Alignment (MSA) can show the relationship between three or more protein or DNA/RNA sequences of a similar length. These alignments are used widely in bioinformatics in order to relate isoforms and homologues of proteins together in environments such as public information clusters that are available on the web.

 

There are several public servers that can handle MSA requests, and each uses a scoring system that judges how similar biological sequences are to each other via various algorithms. These analyse each sequence of amino acids or nucleotides and align conserved regions in the various sequences.

 

We used two different MSA tools: Clustal Omega and MultAlin. They both run different algorithms and so on larger, more complicated sequences where there is less conservation they may produce slightly different alignments. However, here it is useful to see both as they present the data from a different visual perspective.