Question: Protein sequence identity calculation
1
gravatar for ajingnk
5.2 years ago by
ajingnk130
United States
ajingnk130 wrote:

I am new to this field. A little confused about how to define an overall sequence identity between two proteins.

Because one protein can have multiple chains. What I was doing is to compare chain to chain. For protein A and B, I get the maximum similarity for each chain in A to all chains in B, and then get the minimum similarity in all maximum similarities. Or I just conjugate all protein chain sequence to get a whole sequence for that protein.

However, I think I probably should give more credit to long sequence, because short sequence is easier to be similar.

Is there any canonical way to get the identity/similarity score between two protein sequences?

=======================================================================================

And I can also add protein structure information. But for multiple domain proteins, I could not find a score which can scale from 0 to 1, or as easy to understand as sequence identity.

 

Thanks

protein sequence • 3.0k views
ADD COMMENTlink modified 5.1 years ago • written 5.2 years ago by ajingnk130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2021 users visited in the last hour