Calculating Conservation Score From Mutiple Sequence Alignment

Question

[Hari]

I would like to calculate conservation score of amino acids from a multiple sequence alignment,I would like to get a simple 2 column table with residue id and conservation score. I came across Mstatx which can do this but i have problems installing this software. Please do let me know if there are other methods.

Thanks in advance

[bostanict.net]

Hi guys and thanks for the links and comments. Very helpful.

I m wondering if there is any code or stand alone script that can also calculate the score and 4dtv. Any one has it?

thanks

Answer 1

[Michael Schubert]

Do you have to perform this once or multiple times? If it's just once, using a server for calculation and then transforming the result in the desired format will be easier that using a stand-alone application.

There are some web sites that calculate conservation scores, e.g.:

• FRpred (their scoring method FRcons is published in Bioinformatics)
• Jensen-Shannon divergence (also in Bioinformatics)
• ConSurf (algorithm description available in their NAR paper)

[Hari]

Thank you very much,Jensen-Shannon DIvergence very much suits my needs.

[Hari]

Thank you very much JSD works well and it calculates the columnwise conservation score,i would also like to get not only the overall column score but also the score for each amino acids,do you have any idea on this?

[Michael Schubert]

I think "conservation" only makes sense as column-wise score. Otherwise, you could use e.g. % occurence.

[Hari]

I understand this,but i am interested in mapping the conservation onto protein structure,if i have each amino acid(if possible) it will be helpful,do you also have any suggestion as to how i can map this whole conserved region from MSA onto a protein structure?any ideas ?

[Michael Schubert]

You could create a PSSM and then use the amino acid scores for each position.

Answer 2

[Hari]

Although i found JSD,FRpred very helpful to get the conservation score of amino acids,i found even CLustal X has an option to get the conservation score of each amino acid.