Forum:Multiple Sequence Alignment Applications

Question

[manimphil89]

Dear members. I am working in the area of Data mining in Bioinformatics. I need some clarification in computational biology(in specific Multiple sequence alignment (MSA)). What are applications of MSA. And how we extend the output (i.e aligned sequence) to another application. Is it possible to extend the MSA in four phases. Kindly help me in this regard. Thank you in advance..

[Benn]

What are you studying?

Answer 1

[Mensur Dlakic]

Is it possible to extend the MSA in four phases.

It is not clear to me what you mean by this question. I think you need to be more specific if you want more people to respond.

Generally speaking, multiple sequence alignments help us visualize conservation in biological sequences - or lack of it. That sequence conservation implies greater importance as less important parts of DNA and proteins change more due to higher rate of mutations. For example, looking at MSA helps understand what parts of protein are in the catalytic site or near it (marked by circles and triangles in the image below).

If you have a protein structure or its model, conservation can be mapped onto it. In the next image most conserved parts are colored red and least conserved in blue. It should be straightforward to figure out where the catalytic site is.

Beyond visualizations, MSAs can be used to quantify evolutionary relationships between biological sequences, and ultimately between species that carry those sequences, which is depicted in the phylogenetic tree below. Species that are near each other in this tree are closer relatives.

There are many other applications of MSAs that I will not mention here. My final example will be general and without a figure. MSAs can be converted into multidimensional feature vectors that enable us to search for similar patterns in other sequences or genomes. MSA feature vectors are used for numerous machine learning applications in biology.

[Ram]

Please do not use links to lmgtfy - it's not professional and borders on disrespectful. You can instead link to a google search URL.

Also, please use imgbb instead of the hosting site you're using - the DDoS protection on the site you're using causes delays in image loading and leads to user frustration.

[Mensur Dlakic]

I think what you mean to say is that you think it may be not professional and borders on disrespectful. Because telling someone who you don't know and who is trying to help that they are not professional and are disrespectful is the very definition of being unprofessional and disrespectful.

I will do as you suggested next time.