Question: Calculating Conservation Score From Mutiple Sequence Alignment
7
gravatar for Hari
7.8 years ago by
Hari240
Hari240 wrote:

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

scoring multiple • 16k views
ADD COMMENTlink modified 2.7 years ago by bostanict.net0 • written 7.8 years ago by Hari240
10
gravatar for Michael Schubert
7.8 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

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.:

ADD COMMENTlink written 7.8 years ago by Michael Schubert6.9k

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

ADD REPLYlink written 7.8 years ago by Hari240

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?

ADD REPLYlink written 7.8 years ago by Hari240

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

ADD REPLYlink written 7.8 years ago by Michael Schubert6.9k

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 ?

ADD REPLYlink written 7.8 years ago by Hari240

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

ADD REPLYlink written 7.8 years ago by Michael Schubert6.9k
0
gravatar for Hari
7.8 years ago by
Hari240
Hari240 wrote:

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.

ADD COMMENTlink written 7.8 years ago by Hari240
0
gravatar for bostanict.net
2.7 years ago by
bostanict.net0 wrote:

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

ADD COMMENTlink written 2.7 years ago by bostanict.net0
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