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Multiple Sequence Alignment

 This web page was produced as an assignment for bioinformatics at Samford.

What is it?

Multiple Sequence Alignment (MSA) is a bioinformatics technique that allows a person to align three or more biological sequences, either nucleotides or amino acids, of a similar length.  To align two or more sequences means to match up either the nucleotides or amino acids from each sequence in a way that they are paired so that it shows how closely related they are.  Mismatches between two or more sequences are possible and often occur.  One of two options is possible when this happens.  The mismatch can stay where it is or a gap, or space in the sequence, can be put in its place depending on what is more favorable.  Methods and algorithms have been made to determine the best way to align sequences, and whether or not a gap is needed when there is a mismatch of nucleotides or amino acids.  In the bit of aligned sequences below, you can see the green arrow pointing to a mismatch and a red arrow pointing to a gap.

What would you use it for?

MSA is a bioinformatics technique that is very useful.  Having aligned sequences can help reveal areas that are highly conserved, meaning unchanged between each sequence, and areas that are prone to change.  Knowing which areas are highly conserved can give insight to a part of the gene or protein that are very important to its function.  Usually these ares are things such as activation sights on proteins.  If the sequence changed in this area it could cause a mutation making the gene nonfunctional.  MSA can also show how similar two genes are between species.  This information could be useful if a scientist is looking for a good animal model.  If scientists are testing a drug on hemoglobin, they would want a animal that had a nearly identical hemoglobin protein as a human.  They want a near identical match so that when the drug is tested on humans they have a good idea how it will affect them.  One of the biggest uses for MSA is to see how closely related a group of species is.  When making phylogenetic trees, programs will use information obtained from a MSA to figure out what the most closely related species are.

To better understand how to use MSA check out my how to of MUSCLE, a bioinformatics MSA tool.

Pictures from:


April 5 2012

Jason Goebel (contact)

Biology 306

Samford University

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