I am looking at a protein which has close to 200 other family members but I do not seem to be able to identify the closest relatives belonging to the same subgroup. How do I boil it down to max 10 closest relatives?
Hi Malgorzata,
Do you mean closest by sequence? a neighbor-joining tree is a quick way to measure sequence distance between proteins. there are numerous websites that provide free analysis of this sort. for example:
http://www.phylogeny.fr/
Hi, empirically you can use BLAST to get the absolute %AA identities between your proteins and assign them accordingly.
Alternatively, if you have an active site of, say an enzyme, you can assign relativity based on that specific sequence and ignore the rest.
Yes I did mean the AA sequence identity. In fact the protein I am looking at is an enzyme with two domains, leucin-rich repeat and receptor kinase. But there is all 200 of them. Initially I blasted my sequence against ncbi database but all I got back were homologous protein in different species. However, after making the criteria more stringent I now got what I needed.
Thank you for your answers!
phylogeny.fr seems like a nice tool to use when handling multiple sequences. I will probably use it in the future.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Molecular Biological Techniques