What are the amino acid combinations indicated by the symbols in pairwise alignment?
Entering edit mode
17 months ago
sakuRa • 0


Thank you for reading this question. I have a question about symbols as a result of pairwise alignment of amino acid sequences obtained using MAFFT or Clustal omega.

The colon (:) indicates that the amino acids are strongly conserved, even if they have changed. The dots (.) indicate that the amino acids have changed and are weakly preserved.

What is the combination of amino acids that show strong preservation and the combination of amino acids that show weak preservation in PAM250 and BLOSUM64?

I want that list, but I couldn't find it on the web.

ClustW's multiple alignment amino acid combinations are listed on the following pages. However, the amino acids S and A are included in both the well-preserved amino acid combination (STA) and the weak combination (CSA), and this table is unlikely to be used for pairwise alignment.

https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Bioinformatics+Tools+FAQ Item of "What do consensus symbols represent in a Multiple Sequence Alignment?"

alignment pairwise symbols • 689 views

Login before adding your answer.

Traffic: 1724 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6